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[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | code | 2727 |
export waitKeys, getKey
function waitKeys(win::Window, waitTime::Int64)
waitKeys(win, convert(Float64, waitTime))
end
"""
waitKeys(win::Window, waitTime::Float64)
Waits for a predetermined time for a keypress. Returns immediately when a key is pressed
or the timer runs out.
**Inputs:**
* win::Window
* waitTime::Float64 *default is milliseconds*
**Outputs**: returns the character that was pressed
**Limitations**: currently only returns character keys. Arrow keys, tab, return, etc. do not work.
"""
function waitKeys(win::Window, waitTime::Float64)
#println(" win.event: ", win.event)
#println(" win.event value: ", win.event[])
if win.timeScale == "milliseconds"
waitTime /= 1000
end
start = time()
while (time() - start) < waitTime
while Bool(SDL_PollEvent(win.event))
#while( SDL_PollEvent( win.event ) )
event_ref = win.event
evt = event_ref[]
evt_ty = evt.type
evt_text = evt.text
if( evt_ty == SDL_TEXTINPUT )
textTemp = NTupleToString(evt_text.text)
if textTemp != nothing
SDL_StopTextInput()
if textTemp == " " # space
return "space"
elseif textTemp == " " # tab
return "tab"
else
return textTemp
end
end
end
#= if evt_ty == SDL_KEYDOWN
println( "Key press detected (", time() - start,")\n" );
elseif evt_ty == SDL_KEYUP
println( "Key release detected\n" );
end =#
end
end
end
#------------------------------------
"""
getKey(win::Window)
Waits until a key is pressed.
**Inputs:**
* win::Window
**Outputs**: returns the character that was pressed
**Limitations**: currently only returns character keys. Arrow keys, tab, return, etc. do not work.
"""
function getKey(win::Window)
#Enable text input
SDL_StartTextInput();
keypressed = "" # ensures that keypressed is not local the while loop
#win.firstKey = false # couldn't find a way to inject a Key_UP event in the queue, so did this instead
done = false
while done == false
while Bool(SDL_PollEvent(win.event))
event_ref = win.event
evt = event_ref[]
evt_ty = evt.type
evt_text = evt.text
if( evt_ty == SDL_TEXTINPUT )
keypressed = NTupleToString(evt_text.text)
if keypressed != nothing
SDL_StopTextInput()
if keypressed == " " # space
keypressed = "space"
elseif keypressed == " " # tab
keypressed = "tab"
end
done = true
end
end
end
end
# wait for KeyUp first so that we can debounce
done = false
while done == false
while Bool(SDL_PollEvent(win.event))
event_ref = win.event
evt = event_ref[]
evt_ty = evt.type
if( evt_ty == SDL_KEYUP )
done = true
end
end
end
SDL_StopTextInput()
return keypressed
end | PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | code | 53779 | # Might want to make a larger Window for instructions, with buttons for OK and Back (incase they went too fast)
#using .Gtk: draw as GTKdraw
#import Gtk # this prevents namespace collisions between Gtk's draw() and PsychoJL's draw() functions
include("guiUtilityFunctions.jl")
using Dates
export displayMessage, askQuestionDialog, fileOpenDlg, inputDialog, textInputDialog, DlgFromDict
export infoMessage, happyMessage, warningMessage, errorMessage
# make fileOpenDlg actually work
# mask ask dialog look nice
const SDLK_BACKSPACE = 8
const SDLK_RETURN = 13
const SDLK_c = 99
const SDLK_v = 118
const KMOD_CTRL = 192
const SDLK_KP_ENTER = 1073741912
const SDLK_LEFT = 1073741904
const SDLK_RIGHT = 1073741903
#-==========================================================================================================
function fileOpenDlg()
file = Gtk.open_dialog_native("My first file dialog")
filehandle = Gtk.open("$file");
Netlist_lines = Gtk.readlines(filehandle);
Gtk.close(filehandle);
Netlist_lines[1][begin:3]
end
#-=============================================
#
"""
displayMessage( message::String)
Displays a message along with an "OK" button. Use before opening the main window
or after closing the main window. Useful for displaying errors or experiment completion messages.
**Inputs:** PsychoJL Window, String\n
**Outputs:** Nothing\n
"""
function displayMessage( message::String)
SDL_ShowSimpleMessageBox( SDL_MESSAGEBOX_INFORMATION, "Alert", message, C_NULL)
# debounces by waiting for an SDL_KEYUP event
SDLevent = Ref{SDL_Event}()
done = false
while done == false
while Bool(SDL_PollEvent(SDLevent))
event_ref = SDLevent
evt = event_ref[]
evt_ty = evt.type
if( evt_ty == SDL_KEYUP )
done = true
end
end
end
end
#-=============================================
"""
infoMessage( message::String)
Displays a message along with an "OK" button. Use before opening the main window
or after closing the main window. Useful for displaying general information.
**Inputs:** String\n
**Outputs:** Nothing\n
"""
function infoMessage( message::String)
genericMessage(message, "information.png")
end
#-----------------
"""
happyMessage( message::String)
Displays a message along with an "OK" button. Use before opening the main window
or after closing the main window. Useful for experiment completion messages.
**Inputs:** String\n
**Outputs:** Nothing\n
"""
function happyMessage( message::String)
genericMessage(message, "HappyFace.png")
end
#-----------------
"""
warningMessage( message::String)
Displays a message along with an "OK" button. Use before opening the main window
or after closing the main window. Useful for displaying non-critical warnings.
**Inputs:** String\n
**Outputs:** Nothing\n
"""
function warningMessage( message::String)
genericMessage(message, "warning.png")
end
#-----------------
"""
errorMessage( message::String)
Displays a message along with an "OK" button. Use before opening the main window
or after closing the main window. Useful for displaying critical errors.
**Inputs:** String\n
**Outputs:** Nothing\n
"""
function errorMessage( message::String)
genericMessage(message, "error.png")
end
#does SDL do text wrap?
#Even so, I want to use \n to add new lines
#-=============================================
function genericMessage( message::String, imageName::String)
SCREEN_WIDTH = 360
SCREEN_HEIGHT = 125
CENTERX = SCREEN_WIDTH ÷ 2
CENTERY = SCREEN_HEIGHT ÷ 2
buttonClicked = "NoButton"
quit::Bool = false;
mX = Ref{Cint}() # pointers that will receive mouse coordinates
mY = Ref{Cint}()
SDLevent = Ref{SDL_Event}() #Event handler
textColor = SDL_Color(0, 0, 0, 0xFF) #Set text color as black
dialogWin = Window([SCREEN_WIDTH, SCREEN_HEIGHT], false, title = "")
renderer = dialogWin.renderer
gFont = dialogWin.font
if gFont == C_NULL
println("*** Error: gFont is NULL")
end
SDL_PumpEvents() # this erases whatever random stuff was in the backbuffer
SDL_SetRenderDrawColor(dialogWin.renderer, 250, 250, 250, 255)
SDL_RenderClear(dialogWin.renderer)
w = Ref{Cint}()
h = Ref{Cint}()
TTF_SizeText(gFont, message, w::Ref{Cint}, h::Ref{Cint})
label = TextStim(dialogWin, message, [CENTERX + 40, 10 + (1*(h[] + 10)) ], # the centerX * 1.5 seem weird, that's because of retina = 0.75 of width
# label = TextStim(dialogWin, message, [round(Int64, SCREEN_WIDTH *0.8), 10 + (1*(h[] + 10)) ], # the centerX * 1.5 seem weird, that's because of retina = 0.75 of width
#label = TextStim(dialogWin, message, [round(Int64,CENTERX * 1.5), 10 + (1*(h[] + 10)) ], # the centerX * 1.5 seem weird, that's because of retina = 0.75 of width
color = [0, 0, 0],
fontSize = 24,
horizAlignment = -1,
vertAlignment = 1 )
draw(label, wrapLength = round(Int64,SCREEN_WIDTH*1.5)-50 ) # SCREEN_WIDTH seems weird, but retina doubles/halves everything
#---------
# draw alert
parentDir = pwd()
filePath = joinpath(parentDir, "artifacts")
filePath = joinpath(filePath, imageName)
#symbol = ImageStim( dialogWin, filePath, [round(Int64, SCREEN_WIDTH *0.2), CENTERY] )
symbol = ImageStim( dialogWin, filePath, [CENTERX ÷ 1.5, SCREEN_HEIGHT] ) # This might break with retina
draw(symbol, magnification = 0.4)
#---------
# draw OK button
OKtext = TextStim(dialogWin, "OK", [0, 0])
OKbutton = ButtonStim(dialogWin,
#[ 20 + (widestKey), 10 + ((length(labels)+1) * (h[] +10)) ], # was 0.75, buthigh dpi shenanigans
#[ widestKey, h[] + 10],
[ round(Int64, SCREEN_WIDTH *0.8), SCREEN_HEIGHT - (h[] ÷ 2)],
[ (SCREEN_WIDTH ÷ 5) , h[] + 10],
OKtext,
"default")
_, ytemp = OKbutton.pos
ytemp ÷= 2
#OKbutton.pos[2] = ytemp
buttonDraw(OKbutton)
OKmap = ButtonMap(OKbutton, "OK-clicked")
#---------
# Play alert sound
parentDir = pwd()
filePath = joinpath(parentDir, "artifacts")
filePath = joinpath(filePath, "qbeep-10db.wav")
mySound = SoundStim(filePath)
play(mySound)
#---------
while( !quit )
while Bool(SDL_PollEvent(SDLevent)) # Handle events on queue
event_ref = SDLevent
evt = event_ref[]
evt_ty = evt.type
evt_key = evt.key
evt_text = evt.text
evt_mouseClick = evt.button
# We only want to update the input text texture when we need to so we have a flag that keeps track of whether we need to update the texture.
if( evt_ty == SDL_KEYDOWN ) #Special key input
#Handle backspace
if evt_key.keysym.sym == SDLK_RETURN || evt_key.keysym.sym == SDLK_KP_ENTER
SDL_StopTextInput(); #Disable text input
hideWindow(dialogWin)
SDL_RenderPresent( renderer );
closeWinOnly(dialogWin)
return "OK"
end
elseif( evt_ty == SDL_MOUSEBUTTONDOWN ) # new version makes a list of clicked items, and the item with the focus is the winner
x = evt_mouseClick.x
y = evt_mouseClick.y
if (OKmap.rightBottom[1] > x > OKmap.leftTop[1]) && (OKmap.rightBottom[2] > y > OKmap.leftTop[2])
OKmap.state = "clicked"
SDL_StopTextInput(); #Disable text input
hideWindow(dialogWin)
SDL_RenderPresent( renderer );
closeWinOnly(dialogWin)
return "OK"
end
end
end
SDL_SetRenderDrawColor(renderer, 250, 250, 250, 255)
SDL_RenderClear( renderer );
#--------------------------------------------
# Update widgets and such
draw(label, wrapLength = round(Int64,SCREEN_WIDTH*1.5)-50 )
draw(symbol, magnification = 0.4)
#-------------------
#Update screen
if OKmap.state == "unclicked"
buttonDraw(OKmap.button)
elseif OKmap.state == "clicked"
buttonDrawClicked(OKmap.button)
OKmap.state = "unclicked"
quit = true
buttonClicked = OKmap.button.TextStim.textMessage
end
SDL_RenderPresent( renderer );
# check for enter or cancel
end
#-------------- Show stuff
SDL_StopTextInput(); #Disable text input
hideWindow(dialogWin)
SDL_RenderPresent( renderer );
#SDL_DestroyWindow(SDL_Window * Window)
closeWinOnly(dialogWin)
return "OK"
end
#-=============================================
function askQuestionDialog(message::String)
println("askQuestionDialog not implemented yet")
end
#-=============================================
function textInputDialog( promptString::String, defaultText::String)
SCREEN_WIDTH = 350
SCREEN_HEIGHT = 150
DoubleWidth = SCREEN_WIDTH * 2 # I don't know if this is a workaround for Retina or SDL_WINDOW_ALLOW_HIGHDPI, but a 400 pixel width yields 800 pixels
firstRun = true
buttonClicked = "NoButton"
quit::Bool = false;
mX = Ref{Cint}() # pointers that will receive mouse coordinates
mY = Ref{Cint}()
cursorLocation = 0 # after the last character. This is in charachter units, not pixels
# this cycles during each refresh from true to false
onTime = 0 # for timing of cursor blinns
# these are used later to get the size of the text when moving the cursor
w = Ref{Cint}()
h = Ref{Cint}()
SDLevent = Ref{SDL_Event}() #Event handler
textColor = SDL_Color(0, 0, 0, 0xFF) #Set text color as black
InitPsychoJL()
dialogWin = Window(title = "", [SCREEN_WIDTH, SCREEN_HEIGHT], false)
SDLwindow = dialogWin.win
renderer = dialogWin.renderer
#Globals = SDLGlobals(SDLwindow, renderer, LTexture(C_NULL, 0 ,0), LTexture(C_NULL, 0 ,0) )
gFont = dialogWin.font
if gFont == C_NULL
println("*** Error: gFont is NULL")
end
SDL_PumpEvents() # this erases whatever random stuff was in the backbuffer
SDL_RenderClear(renderer) #
TTF_SizeText(gFont, "Abcxyz", w, h)
#-===== Their code:
#The current input text.
#inputText::String = "Some Text";
inputText = defaultText
#TTF_SetFontStyle(gFont, TTF_STYLE_ITALIC)
#Globals.promptTextTexture = loadFromRenderedText(Globals, promptString, textColor, dialogWin.italicFont); # inputText.c_str(), textColor );
#leftX = (SCREEN_WIDTH - Globals.promptTextTexture.mWidth)÷2
promptText = TextStim(dialogWin, promptString, [SCREEN_WIDTH, 20 ], # you would think it would be SCREEN_WIDTH÷2, but hi-res messes it centers at SCREEN_WIDTH÷4.
color = [0, 0, 0],
fontSize = 24,
horizAlignment = 0,
vertAlignment = -1,
style = "italic" )
#TTF_SetFontStyle(gFont, TTF_STYLE_NORMAL )
#Globals.inputTextTexture = loadFromRenderedText(Globals, inputText, textColor, gFont); # inputText.c_str(), textColor );
myInputBox = InputBox(dialogWin,
defaultText,
[35, h[]÷2 + 17],
[ (DoubleWidth - 140)÷2, h[]÷2 + 5],
""
)
#--------- Make buttons
buttonList = []
OKtext = TextStim(dialogWin, "OK", [0, 0])
OKbutton = ButtonStim(dialogWin,
[ round(Int64, SCREEN_WIDTH * 0.75), round(Int64, SCREEN_HEIGHT * 0.75)], # was 0.75, buthigh dpi shenanigans
[ round(Int64, SCREEN_WIDTH * 0.25), 68],
OKtext,
"default")
push!(buttonList, ButtonMap(OKbutton, "OK-clicked") )
CancelText = TextStim(dialogWin, "Cancel", [0, 0])
CancelButton = ButtonStim(dialogWin,
[ round(Int64, SCREEN_WIDTH * 0.25), round(Int64, SCREEN_HEIGHT * 0.75)], # was 0.75, buthigh dpi shenanigans
[ round(Int64, SCREEN_WIDTH * 0.25), 68],
CancelText,
"other")
push!(buttonList, ButtonMap(CancelButton, "Cancel-clicked") )
#---------- end buttons
#---------- Make PopUp
popList = []
myPop = PopUpMenu(dialogWin, [70,100], [100, h[] + 10], ["Cat", "Dog", "Bird"] )
push!(popList, PopUpMap(myPop ) )
#---------- end buttons
#Enable text input
SDL_StartTextInput();
#=
Before we go into the main loop we declare a string to hold our text and render it to a texture. We then call
SDL_StartTextInput so the SDL text input functionality is enabled.
=#
#While application is running
while( !quit )
renderText::Bool = false; # The rerender text flag
while Bool(SDL_PollEvent(SDLevent)) # Handle events on queue
event_ref = SDLevent
evt = event_ref[]
evt_ty = evt.type
evt_key = evt.key
evt_text = evt.text
evt_mouseClick = evt.button
# We only want to update the input text texture when we need to so we have a flag that keeps track of whether we need to update the texture.
if( evt_ty == SDL_KEYDOWN ) #Special key input
#Handle backspace
if( evt_key.keysym.sym == SDLK_BACKSPACE && length(inputText) > 0 )
if (length(inputText) - cursorLocation - 1) >= 0
newString = first(inputText, length(inputText) - cursorLocation - 1)
else
newString = ""
end
println(cursorLocation," ",newString)
inputText = newString * last(inputText, cursorLocation)
#inputText = String(chop(inputText, tail = 1)) # remove last item; chop return a substring, so we have to cast it as String
renderText = true;
cursorLocation += 1 # move cursor as text expands
elseif evt_key.keysym.sym == SDLK_RETURN || evt_key.keysym.sym == SDLK_KP_ENTER
return ["OK", inputText]
elseif evt_key.keysym.sym == SDLK_LEFT
cursorLocation += 1
elseif evt_key.keysym.sym == SDLK_RIGHT
cursorLocation -= 1
if cursorLocation <= 0
cursorLocation = 0
end
end
# SDLK_LEFT, SDLK_RIGHT
# SDLK_LEFT = 1073741904
# SDLK_RIGHT = 1073741903
#=
There are a couple special key presses we want to handle. When the user presses backspace we want to remove the last character
from the string. When the user is holding control and presses c, we want to copy the current text to the clip board using
SDL_SetClipboardText. You can check if the ctrl key is being held using SDL_GetModState.
When the user does ctrl + v, we want to get the text from the clip board using SDL_GetClipboardText. This function returns a
newly allocated string, so we should get this string, copy it to our input text, then free it once we're done with it.
Also notice that whenever we alter the contents of the string we set the text update flag.
=#
#Special text input event
elseif( evt_ty == SDL_TEXTINPUT )
textTemp = NTupleToString(evt_text.text)
if (length(inputText) - cursorLocation ) >= 0
leftString = first(inputText, length(inputText) - cursorLocation )
else
leftString = ""
end
inputText = leftString * textTemp * last(inputText, cursorLocation)
#inputText = inputText * textTemp # * is Julila concatenate
renderText = true;
elseif( evt_ty == SDL_MOUSEBUTTONDOWN )
x = evt_mouseClick.x
y = evt_mouseClick.y
for butMap in buttonList
println(butMap.leftTop,", ",butMap.rightBottom)
if (butMap.rightBottom[1] > x > butMap.leftTop[1]) && (butMap.rightBottom[2] > y > butMap.leftTop[2])
butMap.state = "clicked"
end
end
for popMap in popList
if (popMap.rightBottom[1] > x > popMap.leftTop[1]) && (popMap.rightBottom[2] > y > popMap.leftTop[2])
#popMap.popUp.state = "clicked"
println("pre-state change ", popMap.leftTop,", ",popMap.rightBottom)
stateChange(popMap)
draw(popMap.popUp, [x,y]) # enter pop-up button drawing and selection loop
end
end
#=elseif( evt_ty == SDL_MOUSEBUTTONUP )
x = evt_mouseClick.x
y = evt_mouseClick.y
for popMap in popList
if (popMap.rightBottom[1] > x > popMap.leftTop[1]) && (popMap.rightBottom[2] > y > popMap.leftTop[2])
#popMap.popUp.state = "unclicked"
draw(popMap.popUp, [x,y]) # enter pop-up button drawing and selection loop
end
end
=#
end
end
#=
With text input enabled, your key presses will also generate SDL_TextInputEvents which simplifies things like shift key and caps lock.
Here we first want to check that we're not getting a ctrl and c/v event because we want to ignore those since they are already handled
as keydown events. If it isn't a copy or paste event, we append the character to our input string.
=#
if( renderText ) # Rerender text if needed
if( inputText != "" ) # Text is not empty
#Render new text
#Globals.inputTextTexture = loadFromRenderedText(Globals, inputText, textColor, gFont); # inputText.c_str(), textColor );
draw(myInputBox)
else #Text is empty
#Render space texture
InputBox.valueText = " "
#Globals.inputTextTexture = loadFromRenderedText(Globals, " ", textColor, gFont );
end
end
#=
If the text render update flag has been set, we rerender the texture. One little hack we have here is if we have an empty string,
we render a space because SDL_ttf will not render an empty string.
=#
SDL_SetRenderDrawColor(renderer, 250, 250, 250, 255)
SDL_RenderClear( renderer );
#Render text textures
draw(promptText)
# myInputBox = InputBox( [35, Globals.promptTextTexture.mHeight÷2 + 17],
# [ (DoubleWidth - 140)÷2, Globals.inputTextTexture.mHeight÷2 + 5
# ] )
# drawInputBox(renderer, myInputBox)
#=
SDL_Rect( 70,
floor(Int64,(Globals.promptTextTexture.mHeight)) + 35,
DoubleWidth - 140,
Globals.inputTextTexture.mHeight + 10
)
=#
#=
render(Globals.renderer,
Globals.inputTextTexture,
#40, #floor(Int64,( SCREEN_WIDTH - Globals.inputTextTexture.mWidth ) / 2 ),
#DoubleWidth - (Globals.inputTextTexture.mWidth + 20),
DoubleWidth - 70 - (Globals.inputTextTexture.mWidth + 10),
floor(Int64,(Globals.promptTextTexture.mHeight)) + 40,
Globals.inputTextTexture.mWidth,
Globals.inputTextTexture.mHeight );
=#
#-------------------
# need to get size of text for cursor using cursorLocation
TTF_SizeText(gFont, last(inputText, cursorLocation), w::Ref{Cint}, h::Ref{Cint}) # Ref is used if Julia controls the memory
cursorScootch = w[]
#-------------------
if (time() - onTime) < 1
thickLineRGBA(renderer,
DoubleWidth - 70 - 10 - cursorScootch,
floor(Int64, h[]) + 45,
DoubleWidth - 70 - 10 - cursorScootch,
floor(Int64, h[]) + 75,
3,
0, 0, 0, 255)
cursorBlink = false
elseif 1 < (time() - onTime) < 2 # show during this time
#vlineRGBA(Globals.renderer, DoubleWidth - 70, floor(Int64,(Globals.promptTextTexture.mHeight)), floor(Int64,(Globals.promptTextTexture.mHeight)) + 40, 0, 250, 0, 255);
thickLineRGBA(renderer,
DoubleWidth - 70 - 10 - cursorScootch,
floor(Int64, h[]) + 45,
DoubleWidth - 70 - 10 - cursorScootch,
floor(Int64, h[] ) + 75,
3,
255, 250, 255, 255)
cursorBlink = true
else # reset after 1 cycle
onTime = time()
#println(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> else ", time() - offTime,", ", time() - onTime)
end
#Update screen
for butMap in buttonList # button maps help with managing clicks
if butMap.state == "unclicked"
buttonDraw(butMap.button)
elseif butMap.state == "clicked"
buttonDrawClicked(butMap.button)
butMap.state = "unclicked"
quit = true
buttonClicked = butMap.button.TextStim.textMessage
end
end
#if firstRun == true
SDL_GetMouseState(mX, mY)
draw(myPop, [ mX[], mY[] ] )
firstRun = false
#println("drew popup")
#end
SDL_RenderPresent( renderer );
# check for enter or cancel
end
# At the end of the main loop we render the prompt text and the input text.
SDL_StopTextInput(); #Disable text input
hideWindow(dialogWin)
SDL_RenderPresent( renderer );
#SDL_DestroyWindow(SDL_Window * Window)
closeWinOnly(dialogWin)
return [buttonClicked, inputText]
end
#-=============================================
function textInputDialog(dlgTitle::String, promptString::String, defaultText::String)
SCREEN_WIDTH = 350
SCREEN_HEIGHT = 150
firstRun = true
buttonClicked = "NoButton"
quit::Bool = false;
mX = Ref{Cint}() # pointers that will receive mouse coordinates
mY = Ref{Cint}()
cursorLocation = 0 # after the last character. This is in charachter units, not pixels
cursorPixels = 0 # negative (leftward) pixels from end of string
# this cycles during each refresh from true to false
onTime = 0 # for timing of cursor blinns
offTime = 0
# these are used later to get the size of the text when moving the cursor
w = Ref{Cint}()
h = Ref{Cint}()
SDLevent = Ref{SDL_Event}() #Event handler
textColor = SDL_Color(0, 0, 0, 0xFF) #Set text color as black
InitPsychoJL()
dialogWin = Window(title = dlgTitle, [SCREEN_WIDTH, SCREEN_HEIGHT], false)
SDLwindow = dialogWin.win
renderer = dialogWin.renderer
Globals = SDLGlobals(SDLwindow, renderer, LTexture(C_NULL, 0 ,0), LTexture(C_NULL, 0 ,0) )
gFont = dialogWin.font
#gFont = TTF_OpenFont("/Users/MattPetersonsAccount/Documents/Development/Julia/PsychoJL/sans.ttf", 36); # global font
if gFont == C_NULL
println("*** Error: gFont is NULL")
end
SDL_PumpEvents() # this erases whatever random stuff was in the backbuffer
SDL_RenderClear(Globals.renderer) #
#-===== Their code:
#The current input text.
#inputText::String = "Some Text";
inputText = defaultText
#TTF_SetFontStyle(gFont, TTF_STYLE_ITALIC)
Globals.promptTextTexture = loadFromRenderedText(Globals, promptString, textColor, dialogWin.italicFont); # inputText.c_str(), textColor );
leftX = (SCREEN_WIDTH - Globals.promptTextTexture.mWidth)÷2
promptText = TextStim(dialogWin, promptString, [SCREEN_WIDTH, 20 ], # you would think it would be SCREEN_WIDTH÷2, but hi-res messes it centers at SCREEN_WIDTH÷4.
color = [0, 0, 0],
fontSize = 24,
horizAlignment = 0,
vertAlignment = -1,
style = "italic" )
#TTF_SetFontStyle(gFont, TTF_STYLE_NORMAL )
Globals.inputTextTexture = loadFromRenderedText(Globals, inputText, textColor, gFont); # inputText.c_str(), textColor );
#--------- Make buttons
buttonList = []
OKtext = TextStim(dialogWin, "OK", [0, 0])
OKbutton = ButtonStim(dialogWin,
[ round(Int64, SCREEN_WIDTH * 0.75), round(Int64, SCREEN_HEIGHT * 0.75)], # was 0.75, buthigh dpi shenanigans
[ round(Int64, SCREEN_WIDTH * 0.25), 68],
OKtext,
"default")
push!(buttonList, ButtonMap(OKbutton, "OK-clicked") )
CancelText = TextStim(dialogWin, "Cancel", [0, 0])
CancelButton = ButtonStim(dialogWin,
[ round(Int64, SCREEN_WIDTH * 0.25), round(Int64, SCREEN_HEIGHT * 0.75)], # was 0.75, buthigh dpi shenanigans
[ round(Int64, SCREEN_WIDTH * 0.25), 68],
CancelText,
"other")
push!(buttonList, ButtonMap(CancelButton, "Cancel-clicked") )
#---------- end buttons
#---------- Make PopUp
popList = []
myPop = PopUpMenu(dialogWin, [70,100], [100, Globals.inputTextTexture.mHeight + 10], ["Cat", "Dog", "Bird"] )
# mouse clicks say 14,41 and 57,58
# popUp 20, 75 120, 125 size = 100, 51
# popUpMap 20, 75 120, 125
# new scaled Popmap 10,37 60,62
push!(popList, PopUpMap(myPop ) )
#---------- end buttons
#Enable text input
SDL_StartTextInput();
#=
Before we go into the main loop we declare a string to hold our text and render it to a texture. We then call
SDL_StartTextInput so the SDL text input functionality is enabled.
=#
#While application is running
while( !quit )
renderText::Bool = false; # The rerender text flag
while Bool(SDL_PollEvent(SDLevent)) # Handle events on queue
event_ref = SDLevent
evt = event_ref[]
evt_ty = evt.type
evt_key = evt.key
evt_text = evt.text
evt_mouseClick = evt.button
# We only want to update the input text texture when we need to so we have a flag that keeps track of whether we need to update the texture.
if( evt_ty == SDL_KEYDOWN ) #Special key input
#Handle backspace
if( evt_key.keysym.sym == SDLK_BACKSPACE && length(inputText) > 0 )
if (length(inputText) - cursorLocation - 1) >= 0
newString = first(inputText, length(inputText) - cursorLocation - 1)
else
newString = ""
end
println(cursorLocation," ",newString)
inputText = newString * last(inputText, cursorLocation)
#inputText = String(chop(inputText, tail = 1)) # remove last item; chop return a substring, so we have to cast it as String
renderText = true;
cursorLocation += 1 # move cursor as text expands
elseif evt_key.keysym.sym == SDLK_RETURN || evt_key.keysym.sym == SDLK_KP_ENTER
return ["OK", inputText]
elseif evt_key.keysym.sym == SDLK_LEFT
cursorLocation += 1
elseif evt_key.keysym.sym == SDLK_RIGHT
cursorLocation -= 1
if cursorLocation <= 0
cursorLocation = 0
end
end
# SDLK_LEFT, SDLK_RIGHT
# SDLK_LEFT = 1073741904
# SDLK_RIGHT = 1073741903
#=
There are a couple special key presses we want to handle. When the user presses backspace we want to remove the last character
from the string. When the user is holding control and presses c, we want to copy the current text to the clip board using
SDL_SetClipboardText. You can check if the ctrl key is being held using SDL_GetModState.
When the user does ctrl + v, we want to get the text from the clip board using SDL_GetClipboardText. This function returns a
newly allocated string, so we should get this string, copy it to our input text, then free it once we're done with it.
Also notice that whenever we alter the contents of the string we set the text update flag.
=#
#Special text input event
elseif( evt_ty == SDL_TEXTINPUT )
textTemp = NTupleToString(evt_text.text)
if (length(inputText) - cursorLocation ) >= 0
leftString = first(inputText, length(inputText) - cursorLocation )
else
leftString = ""
end
inputText = leftString * textTemp * last(inputText, cursorLocation)
#inputText = inputText * textTemp # * is Julila concatenate
renderText = true;
elseif( evt_ty == SDL_MOUSEBUTTONDOWN )
x = evt_mouseClick.x
y = evt_mouseClick.y
for butMap in buttonList
println(butMap.leftTop,", ",butMap.rightBottom)
if (butMap.rightBottom[1] > x > butMap.leftTop[1]) && (butMap.rightBottom[2] > y > butMap.leftTop[2])
butMap.state = "clicked"
end
end
for popMap in popList
if (popMap.rightBottom[1] > x > popMap.leftTop[1]) && (popMap.rightBottom[2] > y > popMap.leftTop[2])
#popMap.popUp.state = "clicked"
println("pre-state change ", popMap.leftTop,", ",popMap.rightBottom)
stateChange(popMap)
draw(popMap.popUp, [x,y]) # enter pop-up button drawing and selection loop
end
end
#=elseif( evt_ty == SDL_MOUSEBUTTONUP )
x = evt_mouseClick.x
y = evt_mouseClick.y
for popMap in popList
if (popMap.rightBottom[1] > x > popMap.leftTop[1]) && (popMap.rightBottom[2] > y > popMap.leftTop[2])
#popMap.popUp.state = "unclicked"
draw(popMap.popUp, [x,y]) # enter pop-up button drawing and selection loop
end
end
=#
end
end
#=
With text input enabled, your key presses will also generate SDL_TextInputEvents which simplifies things like shift key and caps lock.
Here we first want to check that we're not getting a ctrl and c/v event because we want to ignore those since they are already handled
as keydown events. If it isn't a copy or paste event, we append the character to our input string.
=#
if( renderText ) # Rerender text if needed
if( inputText != "" ) # Text is not empty
#Render new text
Globals.inputTextTexture = loadFromRenderedText(Globals, inputText, textColor, gFont); # inputText.c_str(), textColor );
else #Text is empty
#Render space texture
Globals.inputTextTexture = loadFromRenderedText(Globals, " ", textColor, gFont );
end
end
#=
If the text render update flag has been set, we rerender the texture. One little hack we have here is if we have an empty string,
we render a space because SDL_ttf will not render an empty string.
=#
SDL_SetRenderDrawColor(renderer, 250, 250, 250, 255)
SDL_RenderClear( renderer );
#Render text textures
DoubleWidth = SCREEN_WIDTH * 2 # I don't know if this is a workaround for Retina or SDL_WINDOW_ALLOW_HIGHDPI, but a 400 pixel width yields 800 pixels
#=
render(Globals.renderer,
Globals.promptTextTexture,
# floor(Int64,DoubleWidth -( DoubleWidth - Globals.promptTextTexture.mWidth ) / 2), #SCREEN_WIDTH -
floor( Int64, SCREEN_WIDTH - (Globals.promptTextTexture.mWidth/2) ),
20,
Globals.promptTextTexture.mWidth,
Globals.promptTextTexture.mHeight );
=#
draw(promptText)
myInputBox = InputBox( [35, Globals.promptTextTexture.mHeight÷2 + 17],
[ (DoubleWidth - 140)÷2, Globals.inputTextTexture.mHeight÷2 + 5
] )
drawInputBox(renderer, myInputBox)
#=
SDL_Rect( 70,
floor(Int64,(Globals.promptTextTexture.mHeight)) + 35,
DoubleWidth - 140,
Globals.inputTextTexture.mHeight + 10
)
=#
render(Globals.renderer,
Globals.inputTextTexture,
#40, #floor(Int64,( SCREEN_WIDTH - Globals.inputTextTexture.mWidth ) / 2 ),
#DoubleWidth - (Globals.inputTextTexture.mWidth + 20),
DoubleWidth - 70 - (Globals.inputTextTexture.mWidth + 10),
floor(Int64,(Globals.promptTextTexture.mHeight)) + 40,
Globals.inputTextTexture.mWidth,
Globals.inputTextTexture.mHeight );
#-------------------
# need to get size of text for curso using cursorLocation
TTF_SizeText(gFont, last(inputText, cursorLocation), w::Ref{Cint}, h::Ref{Cint}) # Ref is used if Julia controls the memory
cursorScootch = w[]
#-------------------
if (time() - onTime) < 1
thickLineRGBA(Globals.renderer,
DoubleWidth - 70 - 10 - cursorScootch,
floor(Int64,(Globals.promptTextTexture.mHeight)) + 45,
DoubleWidth - 70 - 10 - cursorScootch,
floor(Int64,(Globals.promptTextTexture.mHeight)) + 75,
3,
0, 0, 0, 255)
cursorBlink = false
elseif 1 < (time() - onTime) < 2 # show during this time
#vlineRGBA(Globals.renderer, DoubleWidth - 70, floor(Int64,(Globals.promptTextTexture.mHeight)), floor(Int64,(Globals.promptTextTexture.mHeight)) + 40, 0, 250, 0, 255);
thickLineRGBA(Globals.renderer,
DoubleWidth - 70 - 10 - cursorScootch,
floor(Int64,(Globals.promptTextTexture.mHeight)) + 45,
DoubleWidth - 70 - 10 - cursorScootch,
floor(Int64,(Globals.promptTextTexture.mHeight)) + 75,
3,
255, 250, 255, 255)
cursorBlink = true
else # reset after 1 cycle
onTime = time()
#println(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> else ", time() - offTime,", ", time() - onTime)
end
#Update screen
for butMap in buttonList # button maps help with managing clicks
if butMap.state == "unclicked"
buttonDraw(butMap.button)
elseif butMap.state == "clicked"
buttonDrawClicked(butMap.button)
butMap.state = "unclicked"
quit = true
buttonClicked = butMap.button.TextStim.textMessage
end
end
#if firstRun == true
SDL_GetMouseState(mX, mY)
draw(myPop, [ mX[], mY[] ] )
firstRun = false
#println("drew popup")
#end
SDL_RenderPresent( renderer );
# check for enter or cancel
end
# At the end of the main loop we render the prompt text and the input text.
SDL_StopTextInput(); #Disable text input
hideWindow(dialogWin)
SDL_RenderPresent( renderer );
#SDL_DestroyWindow(SDL_Window * Window)
closeWinOnly(dialogWin)
return [buttonClicked, inputText]
end
#-==================================================================================================================
#-==================================================================================================================
#-==================================================================================================================
#=
if key has a dict, its a pull-down menu, else its a text box's default values
- find widest key
- widest key + padding determines width of left column (there needs to be some minimum
- both buttons are as wide as the left column (some minimum width)
- right column is the rest of the screen minus padding
- need to implement ways to change input widget focus
- would love a way to pick TTF from various operating systems
=#
"""
DlgFromDict(dlgDict::Dict)
Displays a dialog box constructed from a dictionary.
**Inputs:** Dictionary defining the input fields (keys) and pre-filled values (values) for the user dialog\n
If the value is a string, that indicates a text input box with a default value.
If the value is a tuple, it indicates that the widget should be pop-up menu populated by the choices listed in the tuple\n
**Outputs:** Dictionary of responses. Keys are from the input dictionary.
Example:
```julia
exp_info = Dict("subject_nr"=>0, "age"=>0, "handedness"=>("right","left","ambi"),
"gender"=>("male","female","other","prefer not to say"))
new_info = DlgFromDict(exp_info)
```
"""
function DlgFromDict(dlgDict::Dict)
DEBUG = true
SCREEN_WIDTH = 350
SCREEN_HEIGHT = 150
firstRun = true
buttonClicked = "NoButton"
quit::Bool = false;
focusedInput = 1 # -99
mX = Ref{Cint}() # pointers that will receive mouse coordinates
mY = Ref{Cint}()
cursorLocation = 0 # after the last character. This is in charachter units, not pixels
cursorPixels = 0 # negative (leftward) pixels from end of string
# this cycles during each refresh from true to false
onTime = 0 # for timing of cursor blinns
offTime = 0
# these are used later to get the size of the text when moving the cursor
w = Ref{Cint}()
h = Ref{Cint}()
SDLevent = Ref{SDL_Event}() #Event handler
textColor = SDL_Color(0, 0, 0, 0xFF) #Set text color as black
# InitPsychoJL() # Is it bad form to call this here?
dialogWin = Window([SCREEN_WIDTH, SCREEN_HEIGHT], false, title = "")
SDLwindow = dialogWin.win
renderer = dialogWin.renderer
#Globals = SDLGlobals(SDLwindow, renderer, LTexture(C_NULL, 0 ,0), LTexture(C_NULL, 0 ,0) )
gFont = dialogWin.font
if gFont == C_NULL
println("*** Error: gFont is NULL")
end
SDL_PumpEvents() # this erases whatever random stuff was in the backbuffer
SDL_SetRenderDrawColor(dialogWin.renderer, 250, 250, 250, 255)
SDL_RenderClear(dialogWin.renderer)
#--- DictDlg really starts here ------------------------
# - find widest key and draw the key labels
widestKey = 20 # arbitrary minimum size
labels = []
i = 1
outDictionary = deepcopy(dlgDict) # we really just want the keys...we'll replace the values later
for (key, value) in dlgDict
TTF_SizeText(gFont, key, w::Ref{Cint}, h::Ref{Cint})
if w[] > widestKey
widestKey = w[]
end
println(key,", ", w[])
label = TextStim(dialogWin, key, [20, 10 + (i*(h[] + 10)) ],
color = [0, 0, 0],
fontSize = 24,
horizAlignment = -1,
vertAlignment = 1 )
push!(labels, label)
i += 1
end
widestKey ÷= 2 # Damn hi-res stuff!
#---------
# draw labels along left side
for label in labels
draw(label)
end
#---------
# draw OK button
buttonList = []
OKtext = TextStim(dialogWin, "OK", [0, 0]; color = "white")
OKbutton = ButtonStim(dialogWin,
#[ 20 + (widestKey), 10 + ((length(labels)+1) * (h[] +10)) ], # was 0.75, buthigh dpi shenanigans
#[ widestKey, h[] + 10],
[ round(Int64, SCREEN_WIDTH *0.8), SCREEN_HEIGHT - (h[] ÷ 2)],
[ (SCREEN_WIDTH ÷ 5) , h[] + 10],
OKtext,
"default")
_, ytemp = OKbutton.pos
ytemp ÷= 2
#OKbutton.pos[2] = ytemp
push!(buttonList, ButtonMap(OKbutton, "OK-clicked") )
buttonDraw(OKbutton)
#---------
# draw Cancel button
Canceltext = TextStim(dialogWin, "Cancel", [0, 0]; color = "black")
CancelButton = ButtonStim(dialogWin,
[ round(Int64, SCREEN_WIDTH *0.5), SCREEN_HEIGHT - (h[] ÷ 2)],
[ (SCREEN_WIDTH ÷ 5) , h[] + 10],
Canceltext,
"other")
_, ytemp = CancelButton.pos
ytemp ÷= 2
#CancelButton.pos[2] = ytemp
push!(buttonList, ButtonMap(CancelButton, "Cancel-clicked") )
buttonDraw(CancelButton)
#-------------
# draw input widgets
inputWidgets = []
inputMapList = []
popUpList = []
i = 0
for (key, value) in dlgDict
leftSide = 40 + widestKey
topSide = 17 + (i*(h[] + 10))
if value isa String || value isa Number # input text box
if value isa Number
value = string(value) # convert numbers to strings
end
if value == ""
value = " " #requires at least one charcters
end
myInputBox = InputBox(dialogWin, value, [leftSide, topSide÷2 ], #-8
[SCREEN_WIDTH - (widestKey + 60), h[]÷2 + 2 ],
key
)
push!(inputWidgets, myInputBox)
push!(inputMapList, InputBoxMap(myInputBox))
draw(myInputBox)
i += 1
elseif value isa Tuple
#leftSide2 = leftSide + ((SCREEN_WIDTH - leftSide)÷2) # input box is top left, this is center
leftSide2 = leftSide + ((SCREEN_WIDTH - (widestKey + 60))÷2) # input box is top left, this is center
leftSide2 *= 2
topSide2 = topSide + h[]÷2
myPop = PopUpMenu(dialogWin,
#[80 + widestKey*2, 20 + (i*(h[] + 10))*2 ], # center pos
#[leftSide2 , topSide2],
[leftSide, topSide ],
[ (SCREEN_WIDTH - (widestKey + 60))*2, (h[]÷2 + 2)*2 ],
collect(value), # collect turns tuple into an array
key )
push!(inputWidgets, myPop)
push!(inputMapList, PopUpMap(myPop ))
push!(popUpList, PopUpMap(myPop ))
draw(myPop, [ -99, -99 ] )
i += 1
end
end
# drawInputBox(renderer, myInputBox)
bend = 0
# wait for KeyUp first so that we can debounce
# but I don't think it will work for this, as dialogWin is not the main window!
# therefore, it contains a different .firstKey!
#=
done = false
while done == false || dialogWin.firstKey == false
while Bool(SDL_PollEvent(SDLevent))
event_ref = SDLevent
evt = event_ref[]
evt_ty = evt.type
if( evt_ty == SDL_KEYUP )
done = true
end
end
end
=#
# win.firstKey = true # couldn't find a way to inject a Key_UP event in the queue, so did this instead
SDL_StartTextInput()
while( !quit )
renderText::Bool = false; # The rerender text flag
while Bool(SDL_PollEvent(SDLevent)) # Handle events on queue
event_ref = SDLevent
evt = event_ref[]
evt_ty = evt.type
evt_key = evt.key
evt_text = evt.text
evt_mouseClick = evt.button
# We only want to update the input text texture when we need to so we have a flag that keeps track of whether we need to update the texture.
if( evt_ty == SDL_KEYDOWN ) #Special key input
#Handle backspace
if typeof(inputWidgets[focusedInput]) == InputBox
if( evt_key.keysym.sym == SDLK_BACKSPACE && length(inputWidgets[focusedInput].valueText) > 0 )
#if (length(inputText) - cursorLocation - 1) >= 0
# newString = first(inputText, length(inputText) - cursorLocation - 1)
if (length(inputWidgets[focusedInput].valueText) - cursorLocation - 1) >= 0
newString = first(inputWidgets[focusedInput].valueText, length(inputWidgets[focusedInput].valueText) - cursorLocation - 1)
else
newString = ""
end
println("\n.........",cursorLocation," ",newString)
inputWidgets[focusedInput].valueText = newString * last(inputWidgets[focusedInput].valueText, cursorLocation)
#inputText = String(chop(inputText, tail = 1)) # remove last item; chop return a substring, so we have to cast it as String
renderText = true;
cursorLocation += 1 # move cursor as text expands
elseif evt_key.keysym.sym == SDLK_LEFT
cursorLocation += 1
elseif evt_key.keysym.sym == SDLK_RIGHT
cursorLocation -= 1
if cursorLocation <= 0
cursorLocation = 0
end
end
end
if evt_key.keysym.sym == SDLK_RETURN || evt_key.keysym.sym == SDLK_KP_ENTER
for inWidgit in inputWidgets
outDictionary[inWidgit.key] = inWidgit.valueText
end
SDL_StopTextInput(); #Disable text input
hideWindow(dialogWin)
SDL_RenderPresent( renderer );
closeWinOnly(dialogWin)
return ["OK", outDictionary]
end
elseif( evt_ty == SDL_TEXTINPUT && typeof(inputWidgets[focusedInput]) == InputBox) #Special text input event
textTemp = NTupleToString(evt_text.text)
if (length(inputWidgets[focusedInput].valueText) - cursorLocation ) >= 0
leftString = first(inputWidgets[focusedInput].valueText, length(inputWidgets[focusedInput].valueText) - cursorLocation )
else
leftString = ""
end
inputWidgets[focusedInput].valueText = leftString * textTemp * last(inputWidgets[focusedInput].valueText, cursorLocation)
#inputText = inputText * textTemp # * is Julila concatenate
renderText = true;
if DEBUG; println("...",inputWidgets[focusedInput].valueText); end
#---------------------------------------------------------------------------------------
#= make list of clicks
determine who gets the click
if clicks > 1
if focus is one of them
focus gets click
else
give error stating that too many widgets got a click
else
widget gets click
act on the click
=#
elseif( evt_ty == SDL_MOUSEBUTTONDOWN ) # new version makes a list of clicked items, and the item with the focus is the winner
x = evt_mouseClick.x
y = evt_mouseClick.y
println("evt_mouseClick.x/y = ",x,", ", y )
for butMap in buttonList
println(butMap.leftTop,", ",butMap.rightBottom)
if (butMap.rightBottom[1] > x > butMap.leftTop[1]) && (butMap.rightBottom[2] > y > butMap.leftTop[2])
butMap.state = "clicked"
end
end
clickedItemIndexes = []
#----------------------
# make list of clicks
for i in eachindex(inputMapList)
inMap = inputMapList[i]
if (inMap.rightBottom[1] > x > inMap.leftTop[1]) && (inMap.rightBottom[2] > y > inMap.leftTop[2])
println("ooooo in a inMap")
println(" ooooo state ", inMap.parent.state )
println(" ooooo typeof ", typeof(inMap.parent))
push!(clickedItemIndexes, i)
end
end
#----------------------
# determine who gets the click
focusClicked = false
focusIndex = -99
for ci in clickedItemIndexes
if inputMapList[ci].parent.focus == true
focusClicked = true
focusIndex = ci
end
end
#----------------------
# if more than one item clicked, use focus as a tie-break (the focused item is expanded and covering another widget).
if length(clickedItemIndexes) > 1
# for now, we assume focus was clicked...but might need to check
if typeof(inputMapList[focusIndex]) == ButtonMap
inputMapList[focusIndex].state = "clicked"
elseif typeof(inputMapList[focusIndex]) == PopUpMap
stateChange(inputMapList[focusIndex])
draw(inputMapList[focusIndex].parent, [x,y])
end
elseif length(clickedItemIndexes) == 1
index = clickedItemIndexes[1]
if typeof(inputMapList[index]) == ButtonMap
inputMapList[i].state = "clicked"
elseif typeof(inputMapList[index]) == PopUpMap
stateChange(inputMapList[index])
draw(inputMapList[index].parent, [x,y])
end
focusedInput = index
for i in eachindex(inputMapList)
if i == focusedInput
inputMapList[i].parent.focus = true
else
inputMapList[i].parent.focus = false
end
end
else
println(".......", evt_ty," ,",typeof(inputWidgets[focusedInput]))
end
end
#=
elseif( evt_ty == SDL_MOUSEBUTTONDOWN )
# new version makes a list of clicked items, and the item with the focus is the winner
x = evt_mouseClick.x
y = evt_mouseClick.y
println("evt_mouseClick.x/y = ",x,", ", y )
clickedItemIndexes = []
for i in eachindex(inputMapList)
inMap = inputMapList[i]
if (inMap.rightBottom[1] > x > inMap.leftTop[1]) && (inMap.rightBottom[2] > y > inMap.leftTop[2])
println("ooooo in a inMap")
println(" ooooo state ", inMap.parent.state )
println(" ooooo typeof ", typeof(inMap.parent))
push!(clickedItemIndexes, i)
end
end
focusFound = false
for i in clickedItemIndexes
if inputMapList[i].parent.focus == true # we found a winner!
focusFound = true
if typeof(inputMapList[i]) == ButtonMap
inputMapList[i].state = "clicked"
elseif typeof(inputMapList[i]) == PopUpMap
stateChange(inputMapList[i])
draw(inputMapList[i].parent, [x,y])
end
elseif focusFound == false # we never found the focus, so go with the only one on the list. If list is>0, send error
if length(clickedItemIndexes) == 1
inMap = inputMapList[i]
# set focus flags
if (inMap.rightBottom[1] > x > inMap.leftTop[1]) && (inMap.rightBottom[2] > y > inMap.leftTop[2])
focusedInput = i
inMap.parent.focus = true
println("focus = ", inMap.leftTop, inMap.rightBottom)
else
inMap.parent.focus = false
we are in a subset of clicked items. Need all so that we can unfocus the others.
end
# do widget specific stuff
if typeof(inputMapList[i]) == ButtonMap
inputMapList[i].state = "clicked"
elseif typeof(inputMapList[i]) == PopUpMap
stateChange(inputMapList[i])
draw(inputMapList[i].parent, [x,y])
end
focusedInput = i
else
#buf =
error("\n*** You have a problem, as two or more widgets received a click \n", clickedItemIndexes,"\n")
end
end
end
end
=#
#-----------------------------------------------------------------------------------------------------
# what about the lines setting and unsetting focus?
# old version below
#=
elseif( evt_ty == SDL_MOUSEBUTTONDOWN )
x = evt_mouseClick.x
y = evt_mouseClick.y
println("evt_mouseClick.x/y = ",x,", ", y )
clickOverlap = false
# skip next part of mouse click overlaps with a popup whose state is "clicked"
for i in eachindex(inputMapList)
inMap = inputMapList[i]
if (inMap.rightBottom[1] > x > inMap.leftTop[1]) && (inMap.rightBottom[2] > y > inMap.leftTop[2])
println("ooooo in a inMap")
println(" ooooo state ", inMap.parent.state )
println(" ooooo typeof ", typeof(inMap.parent))
if inMap.parent.state == "clicked" && typeof(inMap.parent) == PopUpMenu
clickOverlap = true
println(">>>> clickOverlap = true")
stateChange(inMap)
draw(inMap.parent, [x,y]) # CALLED # enter pop-up button drawing and selection loop
end
end
end
if clickOverlap == false # skip these if the mouse click was in an open pop-up
for i in eachindex(inputMapList)
inMap = inputMapList[i]
if (inMap.rightBottom[1] > x > inMap.leftTop[1]) && (inMap.rightBottom[2] > y > inMap.leftTop[2])
focusedInput = i
inMap.parent.focus = true
println("focus = ", inMap.leftTop, inMap.rightBottom)
else
inMap.parent.focus = false
end
end
for butMap in buttonList
if (butMap.rightBottom[1] > x > butMap.leftTop[1]) && (butMap.rightBottom[2] > y > butMap.leftTop[2])
butMap.state = "clicked"
end
end
for popMap in popUpList
if (popMap.rightBottom[1] > x > popMap.leftTop[1]) && (popMap.rightBottom[2] > y > popMap.leftTop[2])
#popMap.popUp.state = "clicked"
println("pre-state change ", popMap.leftTop,", ",popMap.rightBottom)
stateChange(popMap)
println("post-state change ", popMap.leftTop,", ",popMap.rightBottom)
draw(popMap.parent, [x,y]) # CALLED # enter pop-up button drawing and selection loop
end
end
end
println(">>>>>>>>>> button end ", bend)
bend+=1
end # evt_ty == SDL_MOUSEBUTTONDOWN
=#
end
#=
With text input enabled, your key presses will also generate SDL_TextInputEvents which simplifies things like shift key and caps lock.
Here we first want to check that we're not getting a ctrl and c/v event because we want to ignore those since they are already handled
as keydown events. If it isn't a copy or paste event, we append the character to our input string.
=#
if( renderText ) # Rerender text if needed
if typeof(inputWidgets[focusedInput]) == InputBox
if( inputWidgets[focusedInput].valueText != "" ) # Text is not empty
#Render new text
#Globals.inputTextTexture = loadFromRenderedText(Globals, inputText, textColor, gFont); # inputText.c_str(), textColor );
draw(inputWidgets[focusedInput])
else #Text is empty
#Render space texture
inputWidgets[focusedInput].valueText = " "
println("- draw 654: ", focusedInput)
end
end
end
SDL_SetRenderDrawColor(renderer, 250, 250, 250, 255)
SDL_RenderClear( renderer );
#--------------------------------------------
# Update widgets and such
for label in labels
draw(label)
end
for i in eachindex(inputWidgets)
if i != focusedInput # draw the non-focus widgets first
draw(inputWidgets[i]) # CALLED
end
end
if focusedInput != -99 # we do this to make sure any exanded widgets are on top and not drawn over
draw(inputWidgets[focusedInput]) # CALLED
end
#Render text textures
DoubleWidth = SCREEN_WIDTH * 2 # I don't know if this is a workaround for Retina or SDL_WINDOW_ALLOW_HIGHDPI, but a 400 pixel width yields 800 pixels
#=
myInputBox = InputBox( [35, Globals.promptTextTexture.mHeight÷2 + 17],
[ (DoubleWidth - 140)÷2, Globals.inputTextTexture.mHeight÷2 + 5
] )
drawInputBox(renderer, myInputBox)
render(Globals.renderer,
Globals.inputTextTexture,
#40, #floor(Int64,( SCREEN_WIDTH - Globals.inputTextTexture.mWidth ) / 2 ),
#DoubleWidth - (Globals.inputTextTexture.mWidth + 20),
DoubleWidth - 70 - (Globals.inputTextTexture.mWidth + 10),
floor(Int64,(Globals.promptTextTexture.mHeight)) + 40,
Globals.inputTextTexture.mWidth,
Globals.inputTextTexture.mHeight );
=#
#-------------------
if focusedInput > 0 && typeof(inputWidgets[focusedInput]) == InputBox # only blink cursor in a textbox that is the focus
in = inputWidgets[focusedInput]
# need to get size of text for curso using cursorLocation
TTF_SizeText(dialogWin.font,
last(in.valueText, cursorLocation),
w::Ref{Cint},
h::Ref{Cint}) # Ref is used if Julia controls the memory
cursorScootch = w[]
#-------------------
if (time() - onTime) < 1
thickLineRGBA(dialogWin.renderer,
in.textRect.x + in.textRect.w -6 - cursorScootch,
in.textRect.y +10,
in.textRect.x + in.textRect.w -6 - cursorScootch,
in.textRect.y +10 + h[]-10,
3,
255, 0, 0, 255)
cursorBlink = false
elseif 1 < (time() - onTime) < 2 # show during this time
#vlineRGBA(Globals.renderer, DoubleWidth - 70, floor(Int64,(Globals.promptTextTexture.mHeight)), floor(Int64,(Globals.promptTextTexture.mHeight)) + 40, 0, 250, 0, 255);
thickLineRGBA(dialogWin.renderer,
in.textRect.x + in.textRect.w -6 - cursorScootch,
in.textRect.y +10,
in.textRect.x + in.textRect.w -6 - cursorScootch,
in.textRect.y +10 + h[]-10,
3,
255, 250, 255, 255)
cursorBlink = true
else # reset after 1 cycle
onTime = time()
#println(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> else ", time() - offTime,", ", time() - onTime)
end
end
#Update screen
for butMap in buttonList # button maps help with managing clicks
if butMap.state == "unclicked"
buttonDraw(butMap.button)
elseif butMap.state == "clicked"
buttonDrawClicked(butMap.button)
butMap.state = "unclicked"
quit = true
buttonClicked = butMap.button.TextStim.textMessage
end
end
#if firstRun == true
SDL_GetMouseState(mX, mY)
for myPop in popUpList
if myPop.parent.focus == true
draw(myPop.parent, [ mX[], mY[] ] )
end
end
firstRun = false
#println("drew popup")
#end
SDL_RenderPresent( renderer );
# check for enter or cancel
end
#-------------- Show stuff
SDL_StopTextInput(); #Disable text input
hideWindow(dialogWin)
SDL_RenderPresent( renderer );
#SDL_DestroyWindow(SDL_Window * Window)
closeWinOnly(dialogWin)
for inWidgit in inputWidgets
outDictionary[inWidgit.key] = inWidgit.valueText
end
return [buttonClicked, outDictionary]
end
#-=====================================================================================
# Utility functions
#-=====================================================================================
#- GTK versions (unused) =============================================================
#=
function askQuestionDialog(message::String)
Gtk.ask_dialog("Do you like chocolate ice cream?", "Not at all", "I like it") && println("That's my favorite too.")
end
#-===================================================
function inputDialog(message::AbstractString, entry_default::AbstractString)
# input_dialog(message::AbstractString, entry_default::AbstractString, buttons = (("Cancel", 0), ("Accept", 1)), parent = GtkNullContainer())
resp, entry_text = Gtk.input_dialog(message, entry_default) #buttons = (("Cancel", 0), ("Accept", 1)))
return resp, entry_text
end
=#
| PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | code | 6215 | export InputBox
#-==========================================================================================================
mutable struct SDLGlobals
SDLwindow
renderer
inputTextTexture
promptTextTexture
end
#-==========================================================================================================
# more global shit from here: https:# pastebin.com/HvWxcZKv
mutable struct LTexture
# Initialize
mTexture
mWidth
mHeight
end
#-==================================
function NTupleToString(NTuple)
theString::String = ""
i = 1
done = false
while !done
theChar = NTuple[i]
if theChar == 0 # 0 terminated Cstring
done = true
else
theChar = Char(theChar) # convert ascii interger to char
theString = theString * theChar
i += 1
end
end
return theString
end
#-==================================
mutable struct InputBox
win::Window
valueText::String
leftTop::Vector{Int64}
size::Vector{Int64}
focus::Bool
textTexture::LTexture
rightBottom::Vector{Int64}
pos::Vector{Int64}
textRect::SDL_Rect #Ref{SDL_Rect} # for drawing the text
state::String
key::String # dictionary key
function InputBox( win::Window, valueText::String, leftTop::Vector{Int64}, size::Vector{Int64}, key::String = "no-key-given")
# should probably check to see if theses are valid, or flip their order if needed
if valueText == ""
valueText = " "
end
textTexture = loadFromRenderedText(win, valueText, SDL_Color(0,0,0,255))
rightBottom = [ leftTop[1] + size[1],leftTop[2] + size[2] ]
pos = [(leftTop[1] + rightBottom[1])÷2,(leftTop[2] + rightBottom[2])÷2]
textRect = SDL_Rect( leftTop[1] *2 , leftTop[2] *2 , size[1] *2 , size[2] *2 )
new(win, valueText, leftTop, size, false, textTexture, rightBottom, pos, textRect, "unused", key )
end
end
#-==================================
mutable struct InputBoxMap
parent::InputBox
state::String # clicked or not
leftTop::Vector{Int64}
rightBottom::Vector{Int64}
function InputBoxMap( inBox::InputBox)
state = "unclicked"
leftTop = [inBox.pos[1] - inBox.size[1]÷ 2, inBox.pos[2] - inBox.size[2]÷ 2]
#leftTop[1] ÷= 2
#leftTop[2] ÷= 2
rightBottom = [inBox.pos[1] + inBox.size[1]÷ 2, inBox.pos[2] + inBox.size[2]÷ 2]
#rightBottom[1] ÷= 2
#rightBottom[2] ÷= 2
#left = inBox.leftTop[1]# + (in.size[1] ÷2)
#top = inBox.leftTop[2]# + (in.size[2] ÷2)
new(inBox, state, leftTop, rightBottom )
end
end
#-==================================
function draw(in::InputBox) # drawInputBox
# left = in.leftTop[1]# + (in.size[1] ÷2)
# top = in.leftTop[2]# + (in.size[2] ÷2)
# myRect = SDL_Rect( left *2 , top *2 , in.size[1] *2 , in.size[2] *2 )
drawInputBox(in, in.textRect, in.focus)
end
#--
function drawInputBox(in::InputBox, R::SDL_Rect, focus::Bool) #drawInputBox
# first draw filled Rect
SDL_SetRenderDrawColor(in.win.renderer,
255,
255,
255,
255)
SDL_RenderFillRect( in.win.renderer, Ref{SDL_Rect}(R))
# then draw outline
if focus == false
SDL_SetRenderDrawColor(in.win.renderer,
0,
0,
0,
255)
else
SDL_SetRenderDrawColor(in.win.renderer,
0,
0,
255,
255)
end
SDL_RenderDrawRect( in.win.renderer, Ref{SDL_Rect}(R))
#-----------------------------------------------
in.textTexture = loadFromRenderedText(in.win, in.valueText, SDL_Color(0,0,0,255))
render(in.win.renderer,
in.textTexture,
#DoubleWidth - 70 - (Globals.inputTextTexture.mWidth + 10),
#floor(Int64,(Globals.promptTextTexture.mHeight)) + 40,
#R.x, R.y,
convert(Int32, R.x + R.w -6 - in.textTexture.mWidth), # -22
convert(Int32, R.y +8),
#Globals.inputTextTexture.mWidth,
#Globals.inputTextTexture.mHeight
in.textTexture.mWidth,
in.textTexture.mHeight
#R.w, R.h
)
end
#-==========================================================================================================
# from https:# gist.github.com/TomMinor/855879407c5acca83225
# same person, but on github 13 years earlier
#function loadFromRenderedText(Globals::SDLGlobals, textureText::String, textColor::SDL_Color, gFont::Ptr{SimpleDirectMediaLayer.LibSDL2._TTF_Font} )
function loadFromRenderedText(win::Window, textureText::String, textColor::SDL_Color )
# Render text surface
#textSurface = TTF_RenderText_Blended( gFont, textureText, textColor ); # should anti-alias compared to solid?
textSurface = TTF_RenderText_Blended( win.font, textureText, textColor ); # should anti-alias compared to solid?
if( textSurface == C_NULL )
println( "Unable to render text surface! SDL_ttf Error: %s\n", SDL_GetError() ) #TTF_GetError() );
return false;
end
# Create texture from surface pixels
# font_texture = SDL_CreateTextureFromSurface( Globals.renderer, textSurface );
font_texture = SDL_CreateTextureFromSurface( win.renderer, textSurface );
if( font_texture == C_NULL )
println( "Unable to create texture from rendered text! SDL Error: %s\n", SDL_GetError() );
return false;
end
# Get image dimensions
w = Ref{Cint}()
h = Ref{Cint}()
#TTF_SizeText(gFont, textureText, w::Ref{Cint}, h::Ref{Cint}) # Ref is used if Julia controls the memory
TTF_SizeText(win.font, textureText, w::Ref{Cint}, h::Ref{Cint}) # Ref is used if Julia controls the memory
mWidth = w[]
mHeight = h[]
#Get rid of old surface
SDL_FreeSurface( textSurface );
# Return success
tempTextTexture = LTexture(font_texture, mWidth ,mHeight)
return tempTextTexture
end
#-==========================================================================================================
function render(renderer::Ptr{SDL_Renderer}, ltexture::LTexture, x::Int32, y::Int32, mWidth::Int32, mHeight::Int32)
render(renderer, ltexture, convert(Int64, x), convert(Int64, y), mWidth, mHeight)
end
#-----------------
function render(renderer::Ptr{SDL_Renderer}, ltexture::LTexture, x::Int64, y::Int64, mWidth::Int32, mHeight::Int32)
renderQuad = SDL_Rect( x, y, mWidth, mHeight )
SDL_RenderCopyEx( renderer, ltexture.mTexture, C_NULL, Ref{SDL_Rect}(renderQuad), 0.0, C_NULL, SDL_FLIP_NONE );
end | PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | code | 3635 | export imageStim
#-==================================================================
"""
ImageStim()
Constructor for an ImageStim object
**Constructor inputs:**
* win::Window\n
* imageName::String.......*includes path*\n
* pos::Vector{Int64}\n
**Optional constructor inputs:**
* image::Ptr{SDL_Texture}
* width::Int64
* height::Int64
**Methods:**
* draw()
**Notes:**
width and height are automatically calculated during ImageStim construction.
"""
mutable struct ImageStim #{T}
win::Window
imageName::String
pos::PsychoCoords
image::Ptr{SDL_Texture}
width::Int64 # this will need to change to floats for Psychopy height coordiantes
height::Int64
_pos::Vector{Int64}
# opacity::Int64 # these will need to change to floats to handle Psychopy colors
#----------
function ImageStim( win::Window,
imageName::String,
pos::PsychoCoords = [20,20]; # just far enough to be visible
width = 0, # this will need to change to floats for Psychopy height coordiantes
height = 0
# opacity::Int64 = 255 # these will need to change to floats to handle Psychopy colors
)
surface = IMG_Load(imageName) # loads a picture from a file into a surface buffer. Surfaces are usually transfered to something else
image = SDL_CreateTextureFromSurface(win.renderer, surface) # Now we create a texture from our intial surface
if image == C_NULL
error("Could not open image file")
end
SDL_FreeSurface(surface) # Delete the surface, as we no longer need it.
w_ref, h_ref = Ref{Cint}(0), Ref{Cint}(0) # These create C integer pointers: https://docs.julialang.org/en/v1/manual/calling-c-and-fortran-code/
SDL_QueryTexture(image, C_NULL, C_NULL, w_ref, h_ref) # get the attributes of a texture, such as width and height
w, h = w_ref[], h_ref[]
_pos = SDLcoords(win, pos)
#-------
# change the position so that it draws at the center of the image and not the top-left
#pos[1] -= w÷2
#pos[2] -= h÷2
#-------
new(win,
imageName,
pos, # [ round(Int64, winW/2), round(Int64, winH/2)],
image,
w, # this will need to change to floats for Psychopy height coordiantes
h,
_pos
)
end
end
#----------
"""
draw(theImageStim::ImageStim; magnification::Float64)
Draws an ImageStim to the back buffer.
**Inputs:**
* theImageStim::ImageStim
**Optional Inputs:**
* magnification::Float64
"""
function draw(theImageStim::ImageStim; magnification::Float64)
if magnification == 0
centX = theImageStim._pos[1] - theImageStim.width÷2
centY = theImageStim._pos[2] - h÷2
dest_ref = Ref(SDL_Rect(centX, centY, theImageStim.width, theImageStim.height))
else
centX = theImageStim._pos[1] - (theImageStim.width * magnification)÷2
centY = theImageStim._pos[2] - (theImageStim.height * magnification)÷2
dest_ref = Ref(SDL_Rect(centX,
centY,
theImageStim.width * magnification,
theImageStim.height * magnification
)
)
end
# dest_ref[] = SDL_Rect(theImageStim.pos[1], theImageStim.pos[2], theImageStim.width, theImageStim.height)
#println(theImageStim.pos[1],", ",theImageStim.pos[2],", ",theImageStim.width,", ",theImageStim.height)
SDL_RenderCopy(theImageStim.win.renderer, theImageStim.image, C_NULL, dest_ref)
end
#-----------------------
"""
setPos(image::ImageStim, coords::, coordinates)
Set the position of the image, usually the center unless specified otherwise.
See "Setter Functions" in side tab for more information.
"""
function setPos(image::ImageStim, coords::PsychoCoords)
image._pos = SDLcoords(image.win, coords)
image.pos = coords
end | PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | code | 11487 |
export PopUpMenu, PopUpMap
mutable struct PopUpMenu
win::Window
pos::Vector{Int64}
size::Vector{Int64}
options::Array # list of strings that can be selected
selectionIndex::Int64 # index option that is selected
valueText::String # text of option that is selected
#TextStim::TextStim
#type::String # default, other, custom. default can be clicked with enter key
outlineColor::Vector{Int64} # these will need to change to floats to handle Psychopy colors
fillColor::Vector{Int64} # these will need to change to floats to handle Psychopy colors
selectionColor::Vector{Int64}
textColor::Vector{Int64}
selectionTextColor::Vector{Int64}
selectionHeight::Int64
state::String
leftTop::Vector{Int64} # these change when the state changes, reflecting that the menu has grown
rightBottom::Vector{Int64}
fullLT::Vector{Int64} # this is the full size it expands to when clicked.
fullRB::Vector{Int64}
menuTexts::Vector{TextStim}
smallLT::Vector{Int64}
smallRB::Vector{Int64}
horizAlignment::Int64 # -1 for left, 0 for center, +1 for right
vertAlignment::Int64 # -1 aligns at top, 0 for center, +1 aligns at bottom
focus::Bool
key::String # dictionary key
function PopUpMenu( win::Window, pos::Vector{Int64}, size::Vector{Int64}, options::Array, key = "no-key-given"; horizAlignment = -1, vertAlignment = -1)
if vertAlignment == -1 # top anchored
pos[2] += size[2]÷2
elseif vertAlignment == 0 # center anchored
pos[2] = pos[2]
elseif vertAlignment == +1 # bottom anchored
pos[2] -= size[2]÷2
else
error("invalid popUp vertical popUp alignment parameter")
end
#---------
if horizAlignment == -1 # left anchored
pos[1] += size[1]÷2
elseif horizAlignment == 0 # center justification
pos[1] = pos[1]
elseif horizAlignment == +1 # right anchored
pos[1] -= size[1]÷2
else
error("invalid popUp horizontal popUp alignment parameter")
end
state = "unclicked"
leftTop = [ 2*(pos[1] - size[1]÷ 2), pos[2] - size[2]÷ 2]
rightBottom = [leftTop[1] + size[1], leftTop[2] + size[2]]
#rightBottom = [pos[1] + size[1]÷ 2, pos[2] + size[2]÷ 2]
#----- calculate full expanded size
w = Ref{Cint}()
h = Ref{Cint}()
count = length(options)
halfCount = count/2
maxWidth = 0
for opt in options
TTF_SizeText(win.font, opt, w::Ref{Cint}, h::Ref{Cint})
if w[] > maxWidth
maxWidth = w[]
end
end
maxWidth += 10
if maxWidth < size[1] # size is user defined size of the unclicked box
maxWidth = size[1]
end
height = h[] #* length(options[1]) + 10
#=
fullLT = [pos[1] - maxWidth ÷ 2,
pos[2] - height ÷ 2]
fullRB = [pos[1] + maxWidth ÷ 2,
pos[2] + height ÷ 2]
=#
fullLT = [leftTop[1], pos[2] - round(Int64, (height * halfCount)) - 4] # pos[1] - maxWidth ÷ 2,
fullRB = [rightBottom[1], pos[2] + round(Int64, (height * halfCount)) + 4 ] #pos[1] + maxWidth ÷ 2,
#-----
txtColor = [0,0,0,255]
selectTextColor = [255,255,255,255]
selectColor = [64, 135, 247, 255]
background = [250, 250, 250, 255]
selectHeight = height + 4
#-----
menuTexts::Vector{TextStim} = []
for i in eachindex(options) # make text stimuli for each entry
popUpText = TextStim(win, options[i], [0, 0]; color = txtColor)
#popUpText.pos = [leftTop[1] + 4 , pos[2] ]
popUpText.pos = [leftTop[1] + 10 , rightBottom[2]-4 ]
#popUpText.color = txtColor
popUpText.fontSize = 24
popUpText.horizAlignment = -1
popUpText.vertAlignment = +1
#popUpText.style = "bold"
push!(menuTexts, popUpText)
end
#-----
smallLT = leftTop
smallRB = rightBottom
#-----
new(win, pos, size, options, 1, options[1],
[200,200,200,255],
background,
selectColor,
txtColor,
selectTextColor,
selectHeight,
"unclicked",
leftTop, rightBottom,
fullLT, fullRB,
menuTexts,
smallLT, smallRB,
horizAlignment,vertAlignment, # horizAlignment, vertAlignment
false,
key
)
end
end
#----------------------------
function drawPopUpArrows(popUp::PopUpMenu)
verts = [ [-8, -8], [+8, -8], [0, +8]]
verts1 = [ [-8, 2], [0, +10], [+8, 2]]
verts2 = [ [-8, -2], [0, -10], [+8, -2]]
cX = popUp.rightBottom[1] - 19
cY = popUp.pos[2]
for i in 1:(length(verts1)-1)
draw( Line(popUp.win, [cX + verts1[i][1], cY + verts1[i][2]], [cX + verts1[i+1][1], cY + verts1[i+1][2]], width = 4, lineColor = [255,255,255,255] ) )
end
#draw( line(popUp.win, [cX + verts1[3][1], cY + verts1[3][2]], [cX + verts1[1][1], cY + verts1[1][2]], width = 4, lineColor = [255,255,255,255] ) ) # [160,160,255,255]
for i in 1:(length(verts2)-1)
draw( Line(popUp.win, [cX + verts2[i][1], cY + verts2[i][2]], [cX + verts2[i+1][1], cY + verts2[i+1][2]], width = 4, lineColor = [255,255,255,255] ) )
end
#draw( line(popUp.win, [cX + verts2[3][1], cY + verts2[3][2]], [cX + verts2[1][1], cY + verts2[1][2]], width = 4, lineColor = [255,255,255,255] ) ) # [160,160,255,255]
end
#----------------------------
function draw(popUp::PopUpMenu, mousePos::Vector{Int64} = [-99,-99]) # Int32 because that is what SDL returns for coordinates
draw(popUp, [ convert(Int32, mousePos[1]), convert(Int32, mousePos[2]) ] )
end
#--------
# unicode triangle pointing down is \u25BC:
function draw(popUp::PopUpMenu, mousePos::Vector{Int32} ) # Int32 because that is what SDL returns for coordinates
fC = popUp.fillColor
oC = popUp.outlineColor
if popUp.state == "unclicked"
# draw fill
#SDL_SetRenderDrawColor(popUp.win.renderer, fC[1], fC[2], fC[3], fC[4])
#mRect = SDL_Rect(popUp.leftTop[1], popUp.leftTop[2], popUp.size[1], popUp.size[2]) # wacky Julia struct constructor; x,y, widht, height
#SDL_RenderFillRect(popUp.win.renderer, Ref{SDL_Rect}(mRect)) # that addition mess lets me send the rect as a pointer to the rect
aaFilledRoundRectRGBA(popUp.win.renderer,
popUp.leftTop[1] , popUp.leftTop[2], popUp.rightBottom[1], popUp.rightBottom[2],
8,
fC[1], fC[2], fC[3], fC[4])
#---------
# draw outline
if popUp.focus == false
aaRoundRectRGBA(popUp.win.renderer, #roundedRectangleRGBA
popUp.leftTop[1], popUp.leftTop[2], popUp.rightBottom[1], popUp.rightBottom[2],
8,
oC[1], oC[2], oC[3], oC[4])
else
aaRoundRectRGBA(popUp.win.renderer, #roundedRectangleRGBA
popUp.leftTop[1]-1, popUp.leftTop[2]-1, popUp.rightBottom[1]+1, popUp.rightBottom[2]+1,
8,
0, 0, 255, 255)
end
#---------
# draw text ...maybe move this inside the constructor
popUpText = popUp.menuTexts[popUp.selectionIndex] # TextStim(popUp.win, popUp.options[selection], [0, 0])
#popUpText.pos = [popUp.leftTop[1] + 4 , popUp.pos[2] ]
popUpText.pos = [popUp.leftTop[1] + 10 , popUp.rightBottom[2]-4 ]
draw(popUpText)
# ********************
#popUpSymbol = TextStim(popUp.win, "▼", [0, 0])
aaFilledRoundRectRGBA(popUp.win.renderer,
popUp.rightBottom[1] - 36, popUp.leftTop[2]+4, popUp.rightBottom[1]-4, popUp.rightBottom[2]-4,
8,
64, 134, 237, 255)
drawPopUpArrows(popUp)
# ********************
elseif popUp.state == "clicked" # this enters the pop-up button selection loop
# println("I was clicked ", mousePos)
mousePos[1] *= 2 # Hi Res stuff
mousePos[2] *= 2 # Hi Res stuff
#-----------
# find which item is selected
selectedItem = -99 # we don't use popUp.selectionIndex in case coords are out-of-bounds
for i in eachindex(popUp.options)
yCoordTop = popUp.fullLT[2] + (popUp.selectionHeight * (i-1))
yCoordBottom = yCoordTop + popUp.selectionHeight
#[popUp.leftTop[1] + 4 , yCoord ]
if (popUp.rightBottom[1] > mousePos[1] > popUp.leftTop[1]) && (yCoordBottom > mousePos[2] > yCoordTop)
selectedItem = i
popUp.selectionIndex = i
popUp.valueText = popUp.menuTexts[i].textMessage
end
end
#-------------------------
# draw expanded menu
aaFilledRoundRectRGBA(popUp.win.renderer,
popUp.fullLT[1], popUp.fullLT[2], popUp.fullRB[1], popUp.fullRB[2],
8,
fC[1], fC[2], fC[3], fC[4])
#------
# draw outline
if popUp.focus == false
aaRoundRectRGBA(popUp.win.renderer, #roundedRectangleRGBA
popUp.fullLT[1], popUp.fullLT[2], popUp.fullRB[1], popUp.fullRB[2],
8,
oC[1], oC[2], oC[3], oC[4])
else
aaRoundRectRGBA(popUp.win.renderer, #roundedRectangleRGBA
popUp.fullLT[1]-1, popUp.fullLT[2]-1, popUp.fullRB[1]+2, popUp.fullRB[2]+7,
8,
0, 0, 128, 255)
aaRoundRectRGBA(popUp.win.renderer, #roundedRectangleRGBA
popUp.fullLT[1], popUp.fullLT[2], popUp.fullRB[1]+1, popUp.fullRB[2]+6,
8,
127, 127, 255, 255)
aaRoundRectRGBA(popUp.win.renderer, #roundedRectangleRGBA
popUp.fullLT[1]-1, popUp.fullLT[2]-1, popUp.fullRB[1]+1, popUp.fullRB[2]+6,
8,
0, 0, 255, 255)
end
#------
for i in eachindex(popUp.options)
#options[i]
yCoord = popUp.fullLT[2] + (popUp.selectionHeight * (i-1))
#popUp.menuTexts[i].pos = [popUp.leftTop[1] + 4 , yCoord + (popUp.selectionHeight÷2)]
popUp.menuTexts[i].pos[2] = yCoord + (popUp.selectionHeight÷1)
draw(popUp.menuTexts[i])
#println("Ycoord = ", yCoord,", top = ", popUp.fullLT[2],", bottom = ", popUp.fullRB[2])
# set coords of each then draw
if i == selectedItem # highlight selected item
SDL_SetRenderDrawColor(popUp.win.renderer, 0, 0, 255, 64)
mRect = SDL_Rect(popUp.leftTop[1], yCoord, popUp.size[1], popUp.selectionHeight) #popUp.size[2]) # wacky Julia struct constructor; x,y, widht, height
SDL_RenderFillRect(popUp.win.renderer, Ref{SDL_Rect}(mRect)) # that addition mess lets me send the rect as a pointer to the rect
end
end
#-------------------------
# do event loop
#-------------------------
# draw screen
# SDL_RenderPresent( popUp.win.renderer )
else
errString = "invalid popUp menu state. Got: " * popUp.state
error(errString)
end
end
#---------------------------------------------
# popup maps are part of a larger list of buttons that is looped through to
# draw and handle events.
mutable struct PopUpMap
parent::PopUpMenu
state::String # clicked or not
leftTop::Vector{Int64}
rightBottom::Vector{Int64}
function PopUpMap( parent::PopUpMenu)
state = "unclicked"
leftTop = [parent.pos[1] - parent.size[1]÷ 2, parent.pos[2] - parent.size[2]÷ 2]
leftTop[1] ÷= 2
leftTop[2] ÷= 2
rightBottom = [parent.pos[1] + parent.size[1]÷ 2, parent.pos[2] + parent.size[2]÷ 2]
rightBottom[1] ÷= 2
rightBottom[2] ÷= 2
new(parent, state, leftTop, rightBottom )
end
end
#----------------------------
function stateChange(popMap::PopUpMap)
if popMap.state == "clicked"
popMap.state = "unclicked"
popMap.parent.state = "unclicked"
popMap.leftTop = deepcopy(popMap.parent.smallLT) # change size based on state
popMap.leftTop[1] ÷= 2
popMap.leftTop[2] ÷= 2
popMap.rightBottom = deepcopy(popMap.parent.smallRB)
popMap.rightBottom[1] ÷= 2
popMap.rightBottom[2] ÷= 2
else
popMap.state = "clicked"
popMap.parent.state = "clicked"
popMap.leftTop = deepcopy(popMap.parent.fullLT) # change size based on state
popMap.rightBottom = deepcopy(popMap.parent.fullRB)
popMap.leftTop[1] ÷= 2
popMap.leftTop[2] ÷= 2
popMap.rightBottom[1] ÷= 2
popMap.rightBottom[2] ÷= 2
end
println("changed popMap state to ", popMap.state)
end | PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | code | 37926 | #=
Psychopy defines and uses shapes like this:
myRectPy = visual.Rect(win, size = (0.1, 0.1), pos = (x,y), lineColor = (1,1,-1), fillColor = None)
myRectPy.draw()
In Psychopy, shapes are objects.
In PsychoJL, shapes are structs.
myRectJL = rect(myWin, 100, 100, [400,400] ) # width, height, position array, myRectJL is a Rect structure
draw(myRectJL)
=#
export Rect, Ellipse, draw
export Line, Circle, ShapeStim, Polygon
export setColor, setLineColor, setFillColor, setPos
#=
new functions needed:
SetColor
SetPos
also for images
=#
#-==================================================================
"""
Line()
Constructor for a Line object
**Constructor inputs:**
* win::Window\n
* startPoint::Vector{Int64}\n
* endPoint::Vector{Int64}\n
* width::Int64
* lineColor::PsychoColor\n
**Outputs:** None
**Methods:**
* draw()
"""
mutable struct Line
win::Window
startPoint::PsychoCoords
endPoint::PsychoCoords
width::Int64 # this will need to change to floats for Psychopy height coordiantes
lineColor::PsychoColor # these will need to change to floats to handle Psychopy colors
_lineColor::Vector{Int64}
_startPoint::Vector{Int64}
_endPoint::Vector{Int64}
#----------
function Line( win::Window,
startPoint::PsychoCoords = [0,0],
endPoint::PsychoCoords = [10,10];
width::Int64 = 1,
lineColor::PsychoColor = fill(128, (3)), # these will need to change to floats to handle Psychopy colors
# opacity::Int64 = 255 # these will need to change to floats to handle Psychopy colors
)
# might want to add length and orientation
# Int8Color =
if length(endPoint) != 2
message = "endPoint needs two coordinates, got " * String(length(endPoint)) * " instead."
error(message)
end
if length(startPoint) != 2
message = "startPoint needs two coordinates, got " * String(length(startPoint)) * " instead."
error(message)
end
_startPoint = SDLcoords(win, startPoint)
_endPoint = SDLcoords(win, endPoint)
_lineColor = colorToSDL(win, lineColor)
new(win,
startPoint,
endPoint,
width,
lineColor,
_lineColor,
_startPoint,
_endPoint
)
end
end
#----------
function draw(L::Line)
if L.width == 1 # draw a single anti-aliased line
WULinesAlpha(L.win,
convert(Float64, L._startPoint[1]),
convert(Float64, L._startPoint[2]),
convert(Float64, L._endPoint[1]),
convert(Float64, L._endPoint[2]),
convert(UInt8, L._lineColor[1]),
convert(UInt8, L._lineColor[2]),
convert(UInt8, L._lineColor[3]),
convert(UInt8, L._lineColor[4])
)
else
# If we were really cool, we would center even lines by somehow antialiasing the sides
# in order to make the lines look centered at the start point instead of offset.
WULinesAlphaWidth(L.win,
convert(Float64, L._startPoint[1]),
convert(Float64, L._startPoint[2]),
convert(Float64, L._endPoint[1]),
convert(Float64, L._endPoint[2]),
convert(UInt8, L._lineColor[1]),
convert(UInt8, L._lineColor[2]),
convert(UInt8, L._lineColor[3]),
convert(UInt8, L._lineColor[4]),
L.width
)
end
# drawStartPoint(L.win.renderer,L.startPoint[1] ,L.startPoint[2] )
end
#-==========================
"""
setColor(::Line, ::Union{String, Vector{Int64}, Vector{Int64})
Used to update the color of a Line object.
"""
function setColor(line::Line, color::PsychoColor)
line._lineColor = colorToSDL(line.win, color)
end
#-==========================
#--------
function drawStartPoint(renderer::Ptr{SDL_Renderer}, x::Int64, y::Int64)
# 4 points are drawning like the 5 on dice. the missing center one is x, y
SDL_SetRenderDrawColor(renderer, 255, 255, 255, 255);
SDL_RenderDrawPoint(renderer, x-1, y-1)
SDL_RenderDrawPoint(renderer, x-1, y+1)
SDL_RenderDrawPoint(renderer, x+1, y-1)
SDL_RenderDrawPoint(renderer, x+1, y+1)
end
#-==========================
function getLineLength(L::Line)
return sqrt( ((L.startPoint[1] - L.endPoint[1]) ^2) + ((L.startPoint[2] - L.endPoint[2])^2) )
end
#-=====================================================================================================
#=
#- Line2 experiments with using multiple dispatch for coordinate systems
mutable struct Line2
win::Window
startPoint::Vector{Real}
endPoint::Vector{Real}
width::Int64 # this will need to change to floats for Psychopy height coordiantes
lineColor::Vector{Int64} # these will need to change to floats to handle Psychopy colors
_startPoint::Vector{Int64}
_endPoint::Vector{Int64}
#----------
function Line2( win::Window,
startPoint::Vector{Int64} = [0,0],
endPoint::Vector{Int64} = [10,10];
width::Int64 = 1,
lineColor::Vector{Int64} = fill(128, (4)), # these will need to change to floats to handle Psychopy colors
_startPoint::Vector{Int64} = [0,0],
_endPoint::Vector{Int64} = [10,10]
)
if length(endPoint) != 2
message = "endPoint needs two coordinates, got " * String(length(endPoint)) * " instead."
error(message)
end
if length(startPoint) != 2
message = "startPoint needs two coordinates, got " * String(length(startPoint)) * " instead."
error(message)
end
lineColor = colorToSDL(win, lineColor)
new(win,
startPoint,
endPoint,
width,
convert(Vector{Int64},lineColor),
startPoint,
endPoint
)
end
#----------
function Line2( win::Window,
startPoint::Vector{Float64} = [0.1,0.1],
endPoint::Vector{Float64} = [0.2,0.2];
width::Int64 = 1,
lineColor::Vector{Int64} = fill(128, (4)), # these will need to change to floats to handle Psychopy colors
_startPoint::Vector{Int64} = [0,0],
_endPoint::Vector{Int64} = [10,10]
)
if length(endPoint) != 2
message = "endPoint needs two coordinates, got " * String(length(endPoint)) * " instead."
error(message)
end
if length(startPoint) != 2
message = "startPoint needs two coordinates, got " * String(length(startPoint)) * " instead."
error(message)
end
_, displayHeight = getSize(win)
if win.coordinateSpace == "PsychoPy"
_startPoint[1] = round(Int64, (startPoint[1]+0.5) * displayHeight) # convert PsychoPy to Percent coordinates first then percentage to pixels
_startPoint[2] = round(Int64, (-startPoint[2]+0.5) * displayHeight)
_endPoint[1] = round(Int64, (endPoint[1]+0.5) * displayHeight)
_endPoint[2] = round(Int64, (-endPoint[2]+0.5) * displayHeight)
else
_startPoint[1] = round(Int64, startPoint[1] * displayHeight) # convert percentage to pixels
_startPoint[2] = round(Int64, startPoint[2] * displayHeight)
_endPoint[1] = round(Int64, endPoint[1] * displayHeight)
_endPoint[2] = round(Int64, endPoint[2] * displayHeight)
end
new(win,
startPoint,
endPoint,
width,
convert(Vector{Int64},lineColor),
_startPoint,
_endPoint
)
end
end
#----------
#----------
function draw(L::Line2)
if L.width == 1 # draw a single anti-aliased line
WULinesAlpha(L.win,
convert(Float64, L._startPoint[1]),
convert(Float64, L._startPoint[2]),
convert(Float64, L._endPoint[1]),
convert(Float64, L._endPoint[2]),
convert(UInt8, L.lineColor[1]),
convert(UInt8, L.lineColor[2]),
convert(UInt8, L.lineColor[3]),
convert(UInt8, L.lineColor[4])
)
else
# If we were really cool, we would center even lines by somehow antialiasing the sides
# in order to make the lines look centered at the start point instead of offset.
WULinesAlphaWidth(L.win,
convert(Float64, L._startPoint[1]),
convert(Float64, L._startPoint[2]),
convert(Float64, L._endPoint[1]),
convert(Float64, L._endPoint[2]),
convert(UInt8, L.lineColor[1]),
convert(UInt8, L.lineColor[2]),
convert(UInt8, L.lineColor[3]),
convert(UInt8, L.lineColor[4]),
L.width
)
end
end
=#
#-=====================================================================================================
# Floating point version shelved for now, as you can not do multiple dispatch with optional arguments.
"""
Rect()
Constructor for a Rect object
**Constructor inputs:**
* win::Window,
* width::Int64
* height::Int64
* pos::Vector{Int64} **position**
**Optional constructor inputs:**
* units::String......*(default is "pixel"*
* lineWidth::Int64......*(default is 1)*
* lineColor::PsychoColor......*default is (128, 128, 128)*
* fillColor::PsychoColor......*default is (128, 128, 128)*
* ori::Float64 = 0.0......*(orientation in degrees)*
* opacity::Float......*(default is 1.0, indepenent of alpha)*
**Full list of fields**
* win::Window
* width::Int64
* height::Int64
* pos::Vector{Int64}
* units::String
* lineWidth::Int64
* lineColor::PsychoColor
* fillColor::PsychoColor
* ori::Float64
* opacity::Int64
* SDLRect::SDL_Rect
**Methods:**
* draw()
* setLineColor()
* setFillColor()
* setPos()
"""
mutable struct Rect #{T}
win::Window
width::Int64 # this will need to change to floats for Psychopy height coordiantes
height::Int64
pos::PsychoCoords
units::String
lineWidth::Int64 # this will need to change to floats for Psychopy height coordiantes
lineColor::PsychoColor # these will need to change to floats to handle Psychopy colors
fillColor::PsychoColor # these will need to change to floats to handle Psychopy colors
ori::Float64 # The orientation of the stimulus (in degrees).
opacity::Float64 # these will need to change to floats to handle Psychopy colors
SDLRect::SDL_Rect
_lineColor::Vector{Int64}
_fillColor::Vector{Int64}
_pos::Vector{Int64}
#----------
function Rect( win::Window,
width::Int64 = 1,
height::Int64 = 1,
pos::PsychoCoords = [10,10]; # position
units::String = "pixel",
lineWidth::Int64 = 1,
lineColor::PsychoColor = fill(128, (3)), # these will need to change to floats to handle Psychopy colors
fillColor::PsychoColor = fill(128, (3)), # these will be Psychopy colors
ori::Float64 = 0.0,
opacity::Float64 = 1.0 # these will need to change to floats to handle Psychopy colors
)
# NOTE: SDL uses the upper left corner. I'm converting the to the center of the rect like Psychopy
centerX::Int64 = round(pos[1] - (width/2))
centerY::Int64 = round(pos[2] - (height/2))
_pos = [ centerX, centerY]
SDLRect = SDL_Rect(_pos[1], _pos[2], width, height)
_lineColor = colorToSDL(win, lineColor)
_fillColor = colorToSDL(win, fillColor)
#=
if length(lineColor) == 3 # will need to be changed later when other formats can be used
push!(lineColor, 255)
end
if length(fillColor) == 3 # will need to be changed later when other formats can be used
push!(fillColor, 255)
end
=#
new(win,
width ,
height,
pos,
units,
lineWidth,
lineColor, # these will need to change to floats to handle Psychopy colors
fillColor, # these will be Psychopy colors
ori,
opacity, # these will need to change to floats to handle Psychopy colors
SDLRect, # SDL rectangle object
_lineColor,
_fillColor,
_pos
)
end
end
#----------
"""
draw(various shape types)
Draws the shape (Line, Rect, Ellipse, TextStim, etc.) into the back buffer.
Example:
```julia
newRect = Rect(myWin,
100, # width
100, # height
[200,200], # position
lineColor = [255,0,0],
fillColor = [255,128,128]
)
draw(newRect) # in PsychoPy this would have been newRect.draw()
```
"""
function draw(R::Rect)
# first draw filled Rect
SDL_SetRenderDrawColor(R.win.renderer,
R._fillColor[1],
R._fillColor[2],
R._fillColor[3],
round(Int64, R._fillColor[4] * R.opacity ) )
SDL_RenderFillRect( R.win.renderer, Ref{SDL_Rect}(R.SDLRect))
#println("resulting alpha = ", round(Int64, R._fillColor[4] * R.opacity )," ,", R._fillColor[4]," ,", R.opacity)
#println(R._fillColor)
# then draw outline
SDL_SetRenderDrawColor(R.win.renderer,
R._lineColor[1],
R._lineColor[2],
R._lineColor[3],
round(Int64, R._lineColor[4] * R.opacity) )
SDL_RenderDrawRect( R.win.renderer, Ref{SDL_Rect}(R.SDLRect))
end
#-=====================================================================================================
"""
Ellipse()
Constructor for an Ellipse object
**Inputs:**
* win::Window
* pos::Vector{Int64}
* rx::Int64 ......*horizontal radius*
* ry::Int64 ......*vertical radius*
* lineWidth::Int64
* lineColor::PsychoColor
* fillColor::PsychoColor
* fill::Bool ......*fill or not*
**Outputs:** None
**Methods:**
* draw
* setLineColor()
* setFillColor()
* setPos()
"""
mutable struct Ellipse
win::Window
pos::PsychoCoords
rx::Union{Int64, Float64} # Horizontal radius in pixels of the aa-ellipse
ry::Union{Int64, Float64} # vertical radius in pixels of the aa-ellipse
lineWidth::Int64
lineColor::PsychoColor # these will need to change to floats to handle Psychopy colors
fillColor::PsychoColor # these will need to change to floats to handle Psychopy colors
fill::Bool # these will need to change to floats to handle Psychopy colors
_lineColor::Vector{Int64}
_fillColor::Vector{Int64}
_pos::Vector{Int64}
_rx::Int64
_ry::Int64
#aaellipseRGBA
#----------
#MethodError: no method matching Ellipse(::Window, ::Vector{Int64}, ::Int64, ::Int64, ::Int64, ::Vector{Int64}, ::Vector{Int64}, ::Bool)
# Ellipse(::Window, ::Vector{Int64}, ::Int64, ::Int64; lineWidth, lineColor, fillColor, fill)
function Ellipse(win::Window,
pos::PsychoCoords = [10,10], # position
rx::Union{Int64, Float64} = 20, # Horizontal radius in pixels of the aa-ellipse
ry::Union{Int64, Float64} = 10; # vertical radius in pixels of the aa-ellipse
lineWidth::Int64 = 1,
lineColor::PsychoColor = fill(128, (4)), # these will need to change to floats to handle Psychopy colors
fillColor::PsychoColor = fill(128, (4)), # these will be Psychopy colors
fill::Bool = false
)
_lineColor = colorToSDL(win, lineColor)
_fillColor = colorToSDL(win, fillColor)
if win.coordinateSpace != "LT_Pix"
_, displayHeight = getSize(win) # get true height of window
_rx = round(Int64, rx * displayHeight) # convert percent to pixels
_ry = round(Int64, ry * displayHeight) # convert percent to pixels
_pos = SDLcoords(win, pos)
else
_rx = rx
_ry = ry
_pos = pos
end
new(win,
pos,
rx,
ry,
lineWidth,
lineColor, # these will need to change to floats to handle Psychopy colors
fillColor, # these will be Psychopy colors
fill,
_lineColor,
_fillColor,
_pos,
_rx,
_ry
)
end
end
#----------
#MethodError: Cannot `convert` an object of type Int64 to an object of type Vector{Int64}
#Ellipse(win::Window, pos::Vector{Float64}, rx::Int64, ry::Int64; lineWidth::Int64, lineColor::String, fillColor::Vector{Float64}, fill::Bool)
function draw(El::Ellipse)
if El.fill == true
aaFilledEllipseRGBA(El.win.renderer,
El._pos[1],
El._pos[2],
El._rx,
El._ry,
El._fillColor[1],
El._fillColor[2],
El._fillColor[3],
El._fillColor[4])
# I need to check if linecolor exists or has an alpha>0, and then draw the outline
_aaellipseRGBA(El.win.renderer,El._pos[1], El._pos[2], El._rx, El._ry, El._lineColor, El.fill)
end
if El.lineWidth > 1
# we need to anti-alias the outside. When thickness is >1, radius increases by thickness / 2
# outside antialias first
newrX = El._rx + (El.lineWidth ÷ 2) #-1
newrY = El._ry + (El.lineWidth ÷ 2) -1
_aaellipseRGBA(El.win.renderer,El._pos[1]-1, El._pos[2], newrX, newrY, El.lineColor, El.fill)
thickEllipseRGBA(El.win.renderer,
El._pos[1],
El._pos[2],
El._rx,
El._ry,
El._lineColor[1],
El._lineColor[2],
El._lineColor[3],
El._lineColor[4],
El.lineWidth)
# inside antialias first
newrX = El._rx - (El.lineWidth ÷ 2) #+1
newrY = El._ry - (El.lineWidth ÷ 2)
_aaellipseRGBA(El.win.renderer,El._pos[1]-1, El._pos[2], newrX, newrY, El._lineColor, El.fill)
else
_aaellipseRGBA(El.win.renderer,El._pos[1], El._pos[2], El._rx, El._ry, El._lineColor, El.fill)
end
# below is my lame way of drawing a filled ellipse inside an anti-aliased ellipse
# in reality, I show modify aaelipse fill
#=
if El.fill == true # filled
filledEllipseRGBA(El.win.renderer,El.pos[1], El.pos[2], El.rx, El.ry,
convert(UInt8, El.lineColor[1]),
convert(UInt8, El.lineColor[2]),
convert(UInt8, El.lineColor[3]),
convert(UInt8, El.lineColor[4])
)
end
=#
end
#-=====================================================================================================
"""
Circle()
Constructor for an Circle object
**Inputs:**
* win::Window
* pos::Vector{Int64}
* rad::Int64 ......*radius*
* lineWidth::Int64
* lineColor::PsychoColor
* fillColor::PsychoColor
* fill::Bool ......*fill or not*
**Outputs:** None
**Methods:**
* draw()
* setLineColor()
* setFillColor()
* setPos()
"""
mutable struct Circle
win::Window
pos::PsychoCoords
rad::Union{Int64, Float64} # radius in pixels of the aa-ellipse
lineWidth::Int64
lineColor::PsychoColor # these will need to change to floats to handle Psychopy colors
fillColor::PsychoColor # these will need to change to floats to handle Psychopy colors
fill::Bool # these will need to change to floats to handle Psychopy colors
circlesEllipse::Ellipse
_lineColor::Vector{Int64}
_fillColor::Vector{Int64}
_pos::Vector{Int64}
_rad::Int64
function Circle(win::Window,
pos::PsychoCoords = [10,10], # position
rad::Union{Int64, Float64} = 20; # Horizontal radius in pixels of the aa-ellipse
lineWidth::Int64 = 1,
lineColor::PsychoColor = fill(128, (4)), # these will need to change to floats to handle Psychopy colors
fillColor::PsychoColor = fill(128, (4)), # these will be Psychopy colors
fill::Bool = false
)
_lineColor = colorToSDL(win, lineColor)
_fillColor = colorToSDL(win, fillColor)
if win.coordinateSpace != "LT_Pix"
_, displayHeight = getSize(win) # get true height of window
_rad = round(Int64, rad * displayHeight) # convert percent to pixels
_pos = SDLcoords(win, pos)
else
_rad = rad
_pos = pos
end
circlesEllipse = Ellipse(win, pos, rad, rad, lineWidth=lineWidth,lineColor=lineColor,fillColor=fillColor, fill=fill)
new(win,
pos,
rad,
lineWidth,
lineColor, # these will need to change to floats to handle Psychopy colors
fillColor, # these will be Psychopy colors
fill,
circlesEllipse,
_lineColor,
_fillColor,
_pos,
_rad
)
end
end
#----------
function draw(Circ::Circle)
draw(Circ.circlesEllipse)
end
#-=====================================================================================================
# Floating point version shelved for now, as you can not do multiple dispatch with optional arguments.
"""
ShapeStim()
Constructor for a ShapeStim object, which is a polygon defined by vertices.
**Constructor inputs:**
* win::Window,
* vertices::Vector{Vector{Int64}}
**Optional constructor inputs:**
* units::String......*(default is "pixel"*
* lineWidth::Int64......*(default is 1)*
* lineColor::PsychoColor......*default is (128, 128, 128)*
**Full list of fields**
* win::Window
* vertices::Vector{Vector{Int64}}
Example:
*[ [300, 10], [400, 5], [410,150], [320, 100] ,[290, 20] ]*
* units::String
* lineWidth::Int64
* lineColor::PsychoColor
**Methods:**
* draw()
"""
mutable struct ShapeStim #{T}
win::Window
vertices::Vector{Vector{Int64}} #Vector{Int64}
units::String
lineWidth::Int64 # this will need to change to floats for Psychopy height coordiantes
lineColor::PsychoColor # these will need to change to floats to handle Psychopy colors
#----------
function ShapeStim( win::Window,
vertices::Vector{Vector{Int64}} = [[10,10]]; # a single vertex placeholder
units::String = "pixel",
lineWidth::Int64 = 1,
lineColor::PsychoColor = fill(128, (4)), # these will need to change to floats to handle Psychopy colors
)
lineColor = colorToSDL(win, lineColor)
new(win,
vertices,
units,
lineWidth,
lineColor, # these will need to change to floats to handle Psychopy colors
)
end
end
#----------
function draw(S::ShapeStim)
numCoords = length(S.vertices)
if S.lineWidth == 1 # draw a single anti-aliased line
for i in 2:numCoords
WULinesAlpha(S.win,
convert(Float64, S.vertices[i-1][1]),
convert(Float64, S.vertices[i-1][2]),
convert(Float64, S.vertices[i][1]),
convert(Float64, S.vertices[i][2]),
convert(UInt8, S.lineColor[1]),
convert(UInt8, S.lineColor[2]),
convert(UInt8, S.lineColor[3]),
convert(UInt8, S.lineColor[4])
)
end
# close the shape
WULinesAlpha(S.win,
convert(Float64, S.vertices[1][1]),
convert(Float64, S.vertices[1][2]),
convert(Float64, S.vertices[numCoords][1]),
convert(Float64, S.vertices[numCoords][2]),
convert(UInt8, S.lineColor[1]),
convert(UInt8, S.lineColor[2]),
convert(UInt8, S.lineColor[3]),
convert(UInt8, S.lineColor[4])
)
else
# If we were really cool, we would center even lines by somehow antialiasing the sides
# in order to make the lines look centered at the start point instead of offset.
for i in 2:numCoords
WULinesAlphaWidth(S.win,
convert(Float64, S.vertices[i-1][1]),
convert(Float64, S.vertices[i-1][2]),
convert(Float64, S.vertices[i][1]),
convert(Float64, S.vertices[i][2]),
convert(UInt8, S.lineColor[1]),
convert(UInt8, S.lineColor[2]),
convert(UInt8, S.lineColor[3]),
convert(UInt8, S.lineColor[4]),
S.lineWidth
)
# close the shape
WULinesAlphaWidth(S.win,
convert(Float64, S.vertices[1][1]),
convert(Float64, S.vertices[1][2]),
convert(Float64, S.vertices[numCoords][1]),
convert(Float64, S.vertices[numCoords][2]),
convert(UInt8, S.lineColor[1]),
convert(UInt8, S.lineColor[2]),
convert(UInt8, S.lineColor[3]),
convert(UInt8, S.lineColor[4]),
S.lineWidth
)
end
end
end
#-=====================================================================================================
# Floating point version shelved for now, as you can not do multiple dispatch with optional arguments.
"""
Polygon()
Constructor for a regular Polygon object, such as a pentagon or hexagon.
**Constructor inputs:**
* win::Window,
* pos::Vector{Int64}......*[x,y] coordinates of center*
* rad::Int64......*radius*
* sides::Int64
**Optional constructor inputs:**
* units::String......*(default is "pixel"*
* lineWidth::Int64......*(default is 1)*
* lineColor::PsychoColor......*default is (128, 128, 128)*
**Full list of fields**
* win::Window,
* pos::Vector{Int64}
* rad::Int64......*radius*
* sides::Int64
* units::String
* lineWidth::Int64
* lineColor::PsychoColor
**Methods:**
* draw()
"""
mutable struct Polygon #{T}
win::Window
pos::Vector{Int64}
rad::Int64
sides::Int64
units::String
lineWidth::Int64 # this will need to change to floats for Psychopy height coordiantes
lineColor::PsychoColor # these will need to change to floats to handle Psychopy colors
#----------
function Polygon( win::Window,
pos::Vector{Int64} = [10,10], # a single vertex placeholder
rad::Int64 = 10,
sides::Int64 = 5;
units::String = "pixel",
lineWidth::Int64 = 1,
lineColor::PsychoColor = fill(128, (4)) # these will need to change to floats to handle Psychopy colors
)
lineColor = colorToSDL(win, lineColor)
new(win,
pos,
rad,
sides,
units,
lineWidth,
lineColor, # these will need to change to floats to handle Psychopy colors
)
end
end
#----------
function draw(P::Polygon)
# it would be more efficient to initially fill this with pairs of zeros (pre-allocate)
vertices = []
for i in 1:P.sides
x = P.pos[1] + P.rad * sin(2 * pi * i/P.sides) # this is technically wrong, but I swap sine and cos
y = P.pos[2] + P.rad * cos(2 * pi * i/P.sides) # so that their bases will be on the bottom
push!(vertices, [round(Int64, x),round(Int64, y)])
end
if P.lineWidth == 1 # draw a single anti-aliased line
for i in 2:P.sides
WULinesAlpha(P.win,
convert(Float64, vertices[i-1][1]),
convert(Float64, vertices[i-1][2]),
convert(Float64, vertices[i][1]),
convert(Float64, vertices[i][2]),
convert(UInt8, P.lineColor[1]),
convert(UInt8, P.lineColor[2]),
convert(UInt8, P.lineColor[3]),
convert(UInt8, P.lineColor[4])
)
end
# close the shape
WULinesAlpha(P.win,
convert(Float64, vertices[1][1]),
convert(Float64, vertices[1][2]),
convert(Float64, vertices[P.sides][1]),
convert(Float64, vertices[P.sides][2]),
convert(UInt8, P.lineColor[1]),
convert(UInt8, P.lineColor[2]),
convert(UInt8, P.lineColor[3]),
convert(UInt8, P.lineColor[4])
)
else
# If we were really cool, we would center even lines by somehow antialiasing the sides
# in order to make the lines look centered at the start point instead of offset.
for i in 2:P.sides
WULinesAlphaWidth(P.win,
convert(Float64, vertices[i-1][1]),
convert(Float64, vertices[i-1][2]),
convert(Float64, vertices[i][1]),
convert(Float64, vertices[i][2]),
convert(UInt8, P.lineColor[1]),
convert(UInt8, P.lineColor[2]),
convert(UInt8, P.lineColor[3]),
convert(UInt8, P.lineColor[4]),
P.lineWidth
)
# close the shape
WULinesAlphaWidth(P.win,
convert(Float64, vertices[1][1]),
convert(Float64, vertices[1][2]),
convert(Float64, vertices[P.sides][1]),
convert(Float64, vertices[P.sides][2]),
convert(UInt8, P.lineColor[1]),
convert(UInt8, P.lineColor[2]),
convert(UInt8, P.lineColor[3]),
convert(UInt8, P.lineColor[4]),
P.lineWidth
)
end
end
end
#-==========================
"""
setLineColor(various shape types, color)
Sets the outline color for various solid shapes (Rect, Ellipse, Circle, etc.).
NEED link to colors
```
"""
function setLineColor(solidShape::Union{Rect, Ellipse, Circle}, color::PsychoColor)
solidShape._lineColor = colorToSDL(rect.win, color)
end
#-==========
"""
setFillColor(various shape types, color)
Sets the fill color for various solid shapes (Rect, Ellipse, Circle, etc.)
NEED link to colors
```
"""
function setFillColor(solidShape::Union{Rect, Ellipse, Circle}, color::PsychoColor)
solidShape._fillColor = colorToSDL(rect.win, color)
end
#-=====================================================================================================
"""
setPos(solidShape::Union{Rect, Ellipse, Circle, Polygon}, coordinates)
Set the position of the object, usually the center unless specified otherwise.
See "Setter Functions" in side tab for more information.
"""
function setPos(solidShape::Union{Rect, Ellipse, Circle, Polygon}, coords::PsychoCoords)
solidShape._pos = SDLcoords(solidShape.win, coords)
solidShape.pos = coords
if typeof(solidShape) == Circle
solidShape.circlesEllipse._pos = solidShape._pos # update the ellipse owned by the circle
solidShape.circlesEllipse.pos = solidShape.pos # update the ellipse owned by the circle
end
end
#-======================================================================================================================
#-======================================================================================================================
#=
#----------# from https://stackoverflow.com/questions/38334081/how-to-draw-circles-arcs-and-vector-graphics-in-sdl
#draw one quadrant arc, and mirror the other 4 quadrants
function sdl_ellipse(win::Window, x0::Int64, y0::Int64, radiusX::Int64, radiusY::Int64)
# const pi::Float64 = 3.14159265358979323846264338327950288419716939937510
piHalf::Float64 = π / 2.0; # half of pi
#drew 28 lines with 4x4 circle with precision of 150 0ms
#drew 132 lines with 25x14 circle with precision of 150 0ms
#drew 152 lines with 100x50 circle with precision of 150 3ms
precision::Int64 = 27 # precision value; value of 1 will draw a diamond, 27 makes pretty smooth circles.
theta::Float64 = 0; # angle that will be increased each loop
#starting point
x::Int64 = int(radiusX * cos(theta)) #(Float64)radiusX * cos(theta) # start point
y::Int64 = int(radiusY * sin(theta)) #(float)radiusY * sin(theta) # start point
x1::Int64 = x
y1::Int64 = y
#repeat until theta >= 90;
step::Float64 = piHalf/precision #pih/(float)prec; # amount to add to theta each time (degrees)
#for(theta=step; theta <= pih; theta+=step)//step through only a 90 arc (1 quadrant)
for theta in step:step:piHalf # step through only a 90 arc (1 quadrant)
# get new point location
x1 = int(radiusX * cos(theta) + 0.5) # (float)radiusX * cosf(theta) + 0.5; # new point (+.5 is a quick rounding method)
y1 = int(radiusY * sin(theta) + 0.5) # new point (+.5 is a quick rounding method)
# draw line from previous point to new point, ONLY if point incremented
if( (x != x1) || (y != y1) ) #only draw if coordinate changed
SDL_RenderDrawLine(win.renderer, x0 + x, y0 - y, x0 + x1, y0 - y1 ); # quadrant TR
SDL_RenderDrawLine(win.renderer, x0 - x, y0 - y, x0 - x1, y0 - y1 ); # quadrant TL
SDL_RenderDrawLine(win.renderer, x0 - x, y0 + y, x0 - x1, y0 + y1 ); # quadrant BL
SDL_RenderDrawLine(win.renderer, x0 + x, y0 + y, x0 + x1, y0 + y1 ); # quadrant BR
end
# save previous points
x = x1 #; //save new previous point
y = y1 #;//save new previous point
end
# arc did not finish because of rounding, so finish the arc
if(x!=0)
x=0;
SDL_RenderDrawLine(win.renderer, x0 + x, y0 - y, x0 + x1, y0 - y1 ); # quadrant TR
SDL_RenderDrawLine(win.renderer, x0 - x, y0 - y, x0 - x1, y0 - y1 ); # quadrant TL
SDL_RenderDrawLine(win.renderer, x0 - x, y0 + y, x0 - x1, y0 + y1 ); # quadrant BL
SDL_RenderDrawLine(win.renderer, x0 + x, y0 + y, x0 + x1, y0 + y1 ); # quadrant BR
end
end
#-====================================================================
function draw(L::Line)
#=
SDL_SetRenderDrawColor(L.win.renderer,
L.lineColor[1],
L.lineColor[2],
L.lineColor[3],
L.opacity)
SDL_RenderDrawLine( L.win.renderer, L.startPoint[1], L.startPoint[2], L.endPoint[1], L.endPoint[2])
=#
#=
thickLineRGBA( L.win.renderer,
L.startPoint[1],
L.startPoint[2],
L.endPoint[1],
L.endPoint[2],
L.width,
L.lineColor[1],
L.lineColor[2],
L.lineColor[3],
L.lineColor[4],
)
=#
#=
_aalineRGBA(L.win.renderer,
L.startPoint[1],
L.startPoint[2],
L.endPoint[1],
L.endPoint[2],
L.lineColor[1],
L.lineColor[2],
L.lineColor[3],
L.lineColor[4],
true
)
=#
#=
DrawWuLine(L.win.renderer,
L.startPoint[1],
L.startPoint[2],
L.endPoint[1],
L.endPoint[2],
L.lineColor[1],
L.lineColor[2],
L.lineColor[3],
L.lineColor[4]
)
=#
if L.width == 1 # draw a single anti-aliased line
WULinesAlpha(L.win,
convert(Float64, L.startPoint[1]),
convert(Float64, L.startPoint[2]),
convert(Float64, L.endPoint[1]),
convert(Float64, L.endPoint[2]),
convert(UInt8, L.lineColor[1]),
convert(UInt8, L.lineColor[2]),
convert(UInt8, L.lineColor[3]),
convert(UInt8, L.lineColor[4])
)
#= elseif L.width%2 == 0 # even number line width
println("I haven't implemenet even number widths yet, so I'm giving you a line width of 1")
WULinesAlpha(L.win,
convert(Float64, L.startPoint[1]),
convert(Float64, L.startPoint[2]),
convert(Float64, L.endPoint[1]),
convert(Float64, L.endPoint[2]),
≈,
convert(UInt8, L.lineColor[2]),
convert(UInt8, L.lineColor[3]),
convert(UInt8, L.lineColor[4])
) =#
else # odd nubmer will draw width-2 jaggy lines in the middle flanked by anti-aliased versions
println("I'm trying to draw a wide line ", L.width)
deltaY = L.endPoint[2] - L.startPoint[2]
deltaX = L.endPoint[1] - L.startPoint[1]
radians = atan( deltaY / deltaX )
angleDegrees = rad2deg(radians)-90 # yep, that's the pi-symbol for π. Aint Julia cool!
GeometricLength = round(getLineLength(L))
centerX::Int64 = round( (L.startPoint[1] + L.endPoint[1])/2) # average, not local center round(L.width/2)
centerY::Int64 = round( (L.startPoint[2] + L.endPoint[2])/2) # average, not local center round(GeometricLength/2)#
# 120, 825 for average
# 2, 677 for width and height /2
#centerX = convert(Int64, round( L.startPoint[2]/100))
#centerY = L.startPoint[2]
#centerX = 1000
#centerX = L.startPoint[1]
#centerY = L.startPoint[2]
#centerX = L.endPoint[1]
#centerX = L.endPoint[1]
centerX = L.startPoint[1]
centerY = L.startPoint[2]
println("center = ", centerX, ", ", centerY)
println("startPoint = ", L.startPoint[1], ", ", L.startPoint[2])
println("startPoint = ", L.endPoint[1], ", ", L.endPoint[2])
#center = SDL_Point(Cint(centerX), Cint(centerY))
center = SDL_Point(Cint(0), Cint(0))
#center::SDL_Point = [centerX, centerY]
SDL_SetRenderDrawColor(L.win.renderer,
L.lineColor[1],
L.lineColor[2],
L.lineColor[3],
L.lineColor[4])
if L.width > 1 # only one jaggy
#SDL_RenderDrawLine( L.win.renderer, L.startPoint[1], L.startPoint[2], L.endPoint[1], L.endPoint[2])
# (1) create surface the size of the line
lineSurface = SDL_CreateRGBSurface(0, L.width, round(GeometricLength), 32,0,0,0,0)
println("GeometricLength = ", GeometricLength)
SDL_SetSurfaceBlendMode(lineSurface, SDL_BLENDMODE_BLEND)
# (2) Fill the surface with a rect
#destinationRect = SDL_Rect(centerX, centerY, L.width, convert(UInt32, round(GeometricLength)) )
destinationRect = SDL_Rect(L.startPoint[1], L.startPoint[2], L.width, convert(UInt32, round(GeometricLength)) )
tempColor = MakeInt8Color(L.lineColor[1], L.lineColor[2], L.lineColor[3], L.lineColor[4])
# SDL_FillRect(lineSurface::Ptr{SDL_Surface}, Ref{SDL_Rect}(lineRect), convert(UInt32, tempColor) )
SDL_FillRect(lineSurface::Ptr{SDL_Surface}, C_NULL, convert(UInt32, tempColor) ) # C_NULL = fill entire surface
# this next part puts a notch at the Start end
notchColor = MakeInt8Color(0, 0, 0,255)
notchRect = SDL_Rect(0, 10, L.width,20)
SDL_FillRect(lineSurface::Ptr{SDL_Surface}, Ref{SDL_Rect}(notchRect), convert(UInt32, notchColor) ) # C_NULL = fill entire surface
tempSurface = IMG_Load( "sec_hand.png" );
if tempSurface == C_NULL
println("*** error loading texture: sec_hand.png")
println("current directory is ", pwd())
end
tagRect = SDL_Rect(0,0, 100, 4) # used to color code the hands
SDL_FillRect(tempSurface::Ptr{SDL_Surface}, Ref{SDL_Rect}(tagRect), convert(UInt32, tempColor) )
tempSDLTexture = SDL_CreateTextureFromSurface( L.win.renderer, tempSurface );
w_ref, h_ref = Ref{Cint}(0), Ref{Cint}(0) # These create C integer pointers: https://docs.julialang.org/en/v1/manual/calling-c-and-fortran-code/
SDL_QueryTexture(tempSDLTexture, C_NULL, C_NULL, w_ref, h_ref) # get the attributes of a texture, such as width and height
width = w_ref[]
height = h_ref[]
tempRect = SDL_Rect(L.startPoint[1], L.startPoint[2], width, height) # 160, 160
# tempRect = SDL_Rect(centerX, centerY, width, height)
# tempPoint = SDL_Point(centerX, centerY)
# tempPoint = SDL_Point(10, 10)
tempPoint = SDL_Point(10, 10)
angleDegrees2 = angleDegrees + 90 # positve 90 is down
println("angle of line: ", angleDegrees)
println("angle of arrow: ", angleDegrees2, "\n")
SDL_RenderCopyEx( L.win.renderer, tempSDLTexture, C_NULL, Ref{SDL_Rect}(tempRect), angleDegrees2, Ref{SDL_Point}(tempPoint), SDL_FLIP_NONE );
SDL_FreeSurface( tempSurface );
#==#
#If think there is disagreement between the center of lineRect for SDLFillRect and SDL_RenderCopyEx
#function SDL_FillRect(dst, rect, color)
# ccall((:SDL_FillRect, libsdl2), Cint, (Ptr{SDL_Surface}, Ptr{SDL_Rect}, Uint32), dst, rect, color)
# (3) copy it to a texture
lineTexture = SDL_CreateTextureFromSurface(L.win.renderer, lineSurface)
SDL_FreeSurface(lineSurface) # Delete the surface, as we no longer need it.
# (4) rotate it and copy to the window
# SDL_RenderCopyEx(L.win.renderer, lineTexture, C_NULL, C_NULL, angleDegrees, Ref{SDL_Point}(center), SDL_FLIP_NONE)
# SDL_RenderCopyEx(L.win.renderer, lineTexture, Ref{SDL_Rect}(lineRect), Ref{SDL_Rect}(lineRect), angleDegrees, Ref{SDL_Point}(center), SDL_FLIP_NONE)
SDL_RenderCopyEx(L.win.renderer, lineTexture, C_NULL, Ref{SDL_Rect}(destinationRect), angleDegrees, Ref{SDL_Point}(center), SDL_FLIP_NONE)
# SDL_RenderCopyEx( renderer, timeTexture.texture, C_NULL, Ref{SDL_Rect}(timeTexture.rect), timeTexture.angle, Ref{SDL_Point}(timeTexture.center), SDL_FLIP_NONE );
# SDL_RenderCopyEx(L.win.renderer, lineTexture, C_NULL, Ref{SDL_Rect}(destinationRect), angleDegrees, C_NULL, SDL_FLIP_NONE)
# (5) destroy it and clean up
SDL_DestroyTexture(lineTexture) # no longer need the texture, so delete it
end
#=
for inner in 1:L.width -2
should probably countdown from top, middle, bottom...
SDL_RenderDrawLine( L.win.renderer, L.startPoint[1], L.startPoint[2], L.endPoint[1], L.endPoint[2])
end
=#
end
#prinln(startPoint, endPoint)
# thickLineRGBA(renderer, x1, y1, x2, y2, width, r, g, b, a)
end
=# | PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | code | 2599 | export ErrSound, SoundStim, play
"""
SoundStim()
Constructor for a SoundStim object
**Constructor inputs:**
* filePath::string ......**the entire path to the file, including file name and extension**\n
**Outputs:** None
**Methods:** play()
"""
struct SoundStim
filePath::String
soundData::Ptr{Mix_Chunk}
#----------
function SoundStim( filePath::String)
if isfile(filePath)
soundData = Mix_LoadWAV_RW(SDL_RWFromFile(filePath, "rb"), 1)
else
error("$filePath not found")
end
new(filePath,
soundData
)
end
end
#----------
struct ErrSound
soundData::Ptr{Mix_Chunk}
#----------
function ErrSound()
parentDir = pwd()
filePath = joinpath(parentDir, "artifacts")
filePath = joinpath(filePath, "ErrSound-10db.wav")
if isfile(filePath)
soundData = Mix_LoadWAV_RW(SDL_RWFromFile(filePath, "rb"), 1)
else
error("ErrSound() $filePath not found")
end
new(
soundData
)
end
end
#----------
"""
play(sound::SoundStim; repeats::Int64)
Plays a SoundStim
**Inputs:** SoundStim\n
**Optional Inputs:** repeats\n
**Outputs:** None
"""
function play(S::Union{SoundStim, ErrSound}; repeats::Int64 = 0)
Mix_PlayChannel(-1, S.soundData, repeats)
#no method matching unsafe_convert(::Type{Ptr{Mix_Chunk}}, ::typeof(errSound))
end
#-=======================================================
# play(loops=None,
function testSound()
#if(Mix_OpenAudio(44100, MIX_DEFAULT_FORMAT, 1, 1024) < 0)
# println("SDL_mixer could not initialize!", Mix_GetError())
#end
#Load the music
aud_files = dirname(@__FILE__)
parentDir = pwd()
#println("original directory: ", originalDir) # artifacts
#parentDir = splitdir(pwd())[1]
#println("parent directory: ", parentDir) # artifacts
filePath = joinpath(parentDir, "artifacts")
filePath = joinpath(filePath, "ErrSound.wav")
if isfile("$aud_files/beat.wav")
println("FOUND ErrSound.wave AUDIO FILE!!!!!!!!!!!")
end
music = Mix_LoadMUS(filePath)
if (music == C_NULL)
println(">>> >>>", unsafe_string(SDL_GetError() ) )
error("$filePath not found.")
end
errSound = Mix_LoadWAV_RW(SDL_RWFromFile(filePath, "rb"), 1)
Mix_PlayChannel(-1, errSound, 0)
end
#=
scratch = Mix_LoadWAV_RW(SDL_RWFromFile("$aud_files/scratch.wav", "rb"), 1)
high = Mix_LoadWAV_RW(SDL_RWFromFile("$aud_files/high.wav", "rb"), 1)
med = Mix_LoadWAV_RW(SDL_RWFromFile("$aud_files/medium.wav", "rb"), 1)
low = Mix_LoadWAV_RW(SDL_RWFromFile("$aud_files/low.wav", "rb"), 1)
Mix_PlayChannelTimed(-1, med, 0, -1)
Mix_PlayMusic(music, -1)
sleep(1)
Mix_PauseMusic()
sleep(1)
Mix_ResumeMusic()
sleep(1)
Mix_HaltMusic()
=# | PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | code | 16233 | export draw, TextStim, TextStimExp, setColor
#-================================================================================================================
# TextStim
# Ptr{SimpleDirectMediaLayer.LibSDL2._TTF_Font}
"""
TextStim()
Constructor for a TextStim object
**Constructor inputs:**
* win::Window
* textMessage::String.........*default = "future text"*
* pos::Vector{Int64}........*position: default = [10,10]*
**Optional constructor inputs:**
* color::PsychoColor.........*default = (128, 128, 128)*
* fontName::String = "",
* fontSize::Int64 = 12,.........*default = 12*
* scale::Float64 = 1.0,.........*not the same as font size*
* font::Any.........*default is taken from Window*
* horizAlignment::Int64.........*default = -1, 0 = center, +1 = right*
* vertAlignment::Int64 = 1.........*default = 1, 0 = center, -1 = bottom*
* style::String.........*default = "normal", options include "bold" and "italic"*
* orientation.........*orientation in degrees*
**Methods:**
* draw()
**Notes:**
Using different font sizes requires loading them as different fonts. For now it is easier
to load a large version of a font and using *scale* to scale the size of the resulting image.
"""
mutable struct TextStim #{T}
win::Window
textMessage::String # this will need to change to floats for Psychopy height coordiantes
pos::Vector{Int64}
color::PsychoColor # Union of strings, and float and int vectors
fontName::String
fontSize::Int64
scale::Float64
font::Ptr{TTF_Font}
horizAlignment::Int64 # -1 for left, 0 for center, +1 for right
vertAlignment::Int64 # -1 aligns at top, 0 for center, +1 aligns at bottom
style::String # bold, italic, etc.
orientation::Int64
_color::Vector{Int64}
#----------
function TextStim(win::Window,
textMessage::String = "future text",
pos::Vector{Int64} = [10,10];
color::PsychoColor = "white", # these will need to change to floats to handle Psychopy colors
fontName::String = "",
fontSize::Int64 = 12,
scale::Float64 = 1.0,
font::Any = nothing, # font is for internal use and is a pointer to a TTF
horizAlignment::Int64 = -1,
vertAlignment::Int64 = +1,
style::String = "normal",
orientation::Int64 = 0,
_color::Vector{Int64} = fill(128, (4)) # internal SDL color
)
if fontName == ""
font = win.font
else
println("*** Notice: have not implemented loading from system fonts yet")
end
_color = colorToSDL(win, color)
new(win,
textMessage ,
pos,
color,
fontName,
fontSize,
scale,
font, # these will need to change to floats to handle Psychopy colors
horizAlignment,
vertAlignment,
style,
orientation,
_color
)
end
end
#----------
#----------
"""
draw(text::TextStim; wrapLength::Int64)
Draws an TextStim to the back buffer.
**Inputs:**
* text::TextStim
**Optional Inputs:**
* wrapLength::Int64......*in pixels (for now)*
"""
function draw(text::TextStim; wrapLength::Int64 = -1)
if length(text._color) == 4
_color = SDL_Color(text._color[1], text._color[2] , text._color[3], text._color[4])
elseif length(text._color) == 3
_color = SDL_Color(text._color[1], text._color[2] , text._color[3], 255)
else
println("Error in draw(textStim): colors too short, should have length of 3 or 4")
println("Length = ", length(text._color))
println("Values = ", text._color)
end
#-------------------
if text.style == "normal"
text.font = text.win.font
elseif text.style == "italic"
text.font = text.win.italicFont
elseif text.style == "bold"
text.font = text.win.boldFont
else
error("Unrecognized font style. 'normal', 'italic', 'bold', and 'underline' are recognized.")
end
#---------
if wrapLength == -1
surfaceMessage = TTF_RenderUTF8_Blended(text.font, text.textMessage, _color) # text.win.font
Message = SDL_CreateTextureFromSurface(text.win.renderer, surfaceMessage);
#else
# surfaceMessage = TTF_RenderUTF8_Blended_Wrapped(text.font, text.textMessage, color, wrapLength)
end
# now you can convert it into a texture
#@engineerX you can get dimensions of rendered text with TTF_SizeText(TTF_Font *font, const char *text, int *w, int *h)
w = Ref{Cint}()
h = Ref{Cint}()
if wrapLength == -1
TTF_SizeText(text.font, text.textMessage, w::Ref{Cint}, h::Ref{Cint}) # Ref is used if Julia controls the memory
singleHeight = h[]
else
TTF_SizeText(text.font, text.textMessage, w::Ref{Cint}, h::Ref{Cint}) # Ref is used if Julia controls the memory
singleHeight = h[]
#println("conventional width and height are: ", w[],", ",h[]," for the text: ",text.textMessage)
#w[], h[] = ttf_size_utf8_wrappedAI(text.font, text.textMessage, wrapLength)
strings, widths, h[] = wrapText(text.font, text.textMessage, wrapLength)
#println("wrap width and height are: ", w[],", ",h[]," for the text: ",text.textMessage)
end
if text.vertAlignment == -1 # top anchored
y = text.pos[2]
cy = 0
elseif text.vertAlignment == 0 # center anchored
y = text.pos[2] - round(Int64, h[]/2)
cy = h[]÷2
elseif text.vertAlignment == +1 # bottom anchored
y = text.pos[2] - h[]
if y < singleHeight + 5 # enforce a minimum height so it doesn't go off the top.
y = 5
end
cy = h[]
else
error("invalid text vertical text alignment parameter")
end
#---------
if text.horizAlignment == -1 # left anchored
x = text.pos[1]
cx = 0
elseif text.horizAlignment == 0 # center justification
x = text.pos[1] - round(Int64, w[]/2)
cx = w[]÷2
elseif text.horizAlignment == +1 # right anchored
x = text.pos[1] - w[]
cx = w[]
else
error("invalid text horizontal text alignment parameter")
end
#---------
if text.scale != 1 # scale the text. Not the same as changing the font size.
Message_rect = SDL_Rect(x, y, round(Int64, w[] * text.scale), round(Int64, h[] * text.scale) )
else
if wrapLength == -1
Message_rect = SDL_Rect(x, y, w[], h[])
else
Message_rect = SDL_Rect(x, y + h[]÷2, w[], h[])
end
end
#SDL_RenderCopy(text.win.renderer, Message, C_NULL, Ref{SDL_Rect}(Message_rect) ); # &Message_rect)
if text.orientation == 0
if wrapLength == -1
SDL_RenderCopy(text.win.renderer, Message, C_NULL, Ref{SDL_Rect}(Message_rect) ); # &Message_rect)
else
for s in 1:length(strings) # loop through the sub-strings of wrapped text.
surfaceMessage = TTF_RenderUTF8_Blended(text.font, strings[s], _color) # text.win.font
Message = SDL_CreateTextureFromSurface(text.win.renderer, surfaceMessage)
Message_rect = SDL_Rect(x, y + (s-1)*singleHeight, round(Int64, widths[s] * text.scale), round(Int64, singleHeight * text.scale) )
SDL_RenderCopy(text.win.renderer, Message, C_NULL, Ref{SDL_Rect}(Message_rect) )
end
end
else
center = SDL_Point(cx, cy)
SDL_RenderCopyEx(text.win.renderer, Message, C_NULL, Ref{SDL_Rect}(Message_rect), text.orientation, Ref{SDL_Point}(center), SDL_FLIP_NONE)
# SDL_RenderCopyExF( <<< FUTURE WITH FLOATS
end
# Don't forget to free your surface and texture
SDL_FreeSurface(surfaceMessage);
SDL_DestroyTexture(Message);
end
#----------
"""
setColor(text::TextStim; color::Union{String, Vector{Int64}, Vector{Float64}})
Update the textStim's color
**Inputs:**
* text::TextStim
* color is a string, Vector of integers, or vector of floats.
NEED A LINK TO THE COLORS PAGE
"""
function setColor(text::TextStim, color::PsychoColor)
text._color = colorToSDL(text.win, color)
end
#----------
function setSize(text::TextStim, fontSize::Int64)
println("setSize(::TextStim, fontsize) is a future placeholder for loading a font of the specific size")
end
#----------
function setFont(text::TextStim, fontName::String)
println("setFont(::TextStim, fontName) is a future placeholder for loading a font of the specified name")
end
#-------------------------------
const lineSpace = 2;
#-=============================================================================
function character_is_delimiter(c::Char, delimiters)
for d in delimiters
if c == d
return true
end
end
return false
end
#-=============================================================================
# returns a list of strings for plotting, as well as the resulting width and height
function wrapText(font, original::String, wrapWidth)
if wrapWidth <= 0
error("wrapWidth must be > 0")
end
line_space = 2
strings = []
w = Ref{Cint}()
h = Ref{Cint}()
TTF_SizeText(font, original, w, h) # Ref is used if Julia controls the memory
#-------------------
# return if string does not need to be wrapped
if w[] < wrapWidth
push!(strings, original)
return strings, w[], h[]
end
#-------------------
wrap_delims = [' ', '\t', '\r', '\n']
lineBreak_delims = ['\r', '\n']
currentStr = original
startSpot = 1
endSpot = length(original)
done = false
c = 1
lastFound = 1
while done == false
currentChar = currentStr[c]
if character_is_delimiter(currentChar, wrap_delims) == true
TTF_SizeText(font, currentStr[startSpot:c], w, h)
if character_is_delimiter(currentChar, lineBreak_delims) == true # line break
if lastFound == 1
push!(strings, currentStr[startSpot:c-1])
currentStr = currentStr[c+1:endSpot]
else
push!(strings, currentStr[startSpot:c-1] ) #lastFound-1])
currentStr = currentStr[c+1:endSpot] #lastFound+1:endSpot]
end
endSpot = length(currentStr)
lastFound = 1
c = 0
TTF_SizeText(font, currentStr[1:endSpot], w, h) # check to see if the next string is short enough
if w[] < wrapWidth
done = true
push!(strings, currentStr)
c = endSpot
end
elseif w[] <= wrapWidth
lastFound = c
elseif w[] > wrapWidth
push!(strings, currentStr[startSpot:lastFound-1])
currentStr = currentStr[lastFound+1:endSpot]
endSpot = length(currentStr)
lastFound = 1
c = 0
TTF_SizeText(font, currentStr[1:endSpot], w, h) # check to see if the next string is short enough
if w[] < wrapWidth
done = true
push!(strings, currentStr)
c = endSpot
end
end
end
c += 1
if c >= endSpot
done = true
TTF_SizeText(font, currentStr[startSpot:c-1], w, h)
if w[] > wrapWidth
push!(strings, currentStr[startSpot:lastFound-1])
currentStr = currentStr[lastFound+1:endSpot]
push!(strings, currentStr)
end
end
end
returnWidth = 0
widths = []
# this is written to return max width, but instead we are returning widths of each string
for s in strings
TTF_SizeText(font, s, w, h)
push!(widths, w[])
if w[] > returnWidth
returnWidth = w[]
end
end
returnHeight = h[] + (length(strings) - 1) * (h[] + line_space)
return strings, widths, returnHeight
end
#=
function wrapTextBackwards(font, original::String, wrapWidth)
if wrapWidth <= 0
error("wrapWidth must be > 0")
end
strings = []
w = Ref{Cint}()
h = Ref{Cint}()
TTF_SizeText(font, original, w, h) # Ref is used if Julia controls the memory
#-------------------
# return if string does not need to be wrapped
if w[] < wrapWidth
push!(strings, original)
return strings, w[], h[]
end
#-------------------
wrap_delims = [' ', '\t', '\r', '\n']
lineBreak_delims = ['\r', '\n']
currentStr = original
startSpot = 1
endSpot = length(original)
done = false
c = endSpot
while done == false
#for c in endSpot:-1:startSpot # work backwards, find a delimiter, and if <, add to strings[]
currentChar = currentStr[c]
if character_is_delimiter(currentChar, wrap_delims) == true
TTF_SizeText(font, currentStr[startSpot:c], w, h)
if character_is_delimiter(currentChar, lineBreak_delims) == true # line break
push!(strings, currentStr[startSpot:c-1])
currentStr = currentStr[c+1:endSpot]
endSpot = length(currentStr)
c = endSpot+1
TTF_SizeText(font, currentStr[startSpot:c-1], w, h) # check to see if the next string is short enough
if w[] < wrapWidth
done = true
push!(strings, currentStr)
c = 0
end
elseif w[] < wrapWidth
push!(strings, currentStr[startSpot:c-1])
currentStr = currentStr[c+1:endSpot]
endSpot = length(currentStr)
c = endSpot+1
TTF_SizeText(font, currentStr[startSpot:c-1], w, h) # check to see if the next string is short enough
if w[] < wrapWidth
done = true
push!(strings, currentStr)
c = 0
end
end
end
c -= 1
#end
if c== 0
done = true
push!(strings, currentStr)
end
end
return strings, w[], h[]
end
=#
#=
find delimiter. break on delimiter < length. make new string for next line. return strings.
rules: break on a delimeter
must break on \r or \n
1) scan for delims
2)if no delim is found, find length of string.
If too big:
a) chop at the 2nd-last char
b) add a hyphen
c) add left side to Strings
d) make ride side the next thing to scan
3) if delim is < width, scan until you find the next that is not or find the end.
wrap_delims = [' ', '\t', '\r', '\n']
break_delims = ['\r', '\n']
findfirst(isequal('\n'), str[tok:end])
Strings = []
done = false
while done = false
end
return strings, width, height
=#
#=
mutable struct TextStim #{T}
win::Window
textMessage::String # this will need to change to floats for Psychopy height coordiantes
pos::Vector{Int64}
color::Vector{Int64} # these will need to change to floats to handle Psychopy colors
fontName::String
fontSize::Int64
scale::Float64
font::Ptr{TTF_Font}
horizAlignment::Int64 # -1 for left, 0 for center, +1 for right
vertAlignment::Int64 # -1 aligns at top, 0 for center, +1 aligns at bottom
style::String # bold, italic, etc.
orientation::Int64
end
#----------
function textStim(win::Window,
textMessage::String = "future text",
pos::Vector{Int64} = [10,10];
color::Vector{Int64} = fill(128, (3)), # these will need to change to floats to handle Psychopy colors
fontName::String = "",
fontSize::Int64 = 12,
scale::Float64 = 1.0,
font::Any = nothing, # font is for internal use and is a pointer to a TTF
horizAlignment::Int64 = 1,
vertAlignment::Int64 = 1,
style::String = "normal",
orientation::Int64 = 0
)
if fontName == ""
font = win.font
else
println("*** Notice: have not implemented loading from system fonts yet")
end
textStruct = TextStim(win,
textMessage ,
pos,
color,
fontName,
fontSize,
scale,
font, # these will need to change to floats to handle Psychopy colors
horizAlignment,
vertAlignment,
style,
orientation
)
return textStruct
end
=#
mutable struct TextStimExp
win::Window
textMessage::String # this will need to change to floats for Psychopy height coordiantes
pos::Vector{Int64}
color::PsychoColor # these will need to change to floats to handle Psychopy colors
fontName::String
fontSize::Int64
scale::Float64
font::Ptr{TTF_Font}
horizAlignment::Int64 # -1 for left, 0 for center, +1 for right
vertAlignment::Int64 # -1 aligns at top, 0 for center, +1 aligns at bottom
style::String # bold, italic, etc.
orientation::Int64
#----------
function TextStimExp(win::Window,
textMessage::String = "future text",
pos::Vector{Int64} = [10,10];
color::PsychoColor = fill(128, (3)), # these will need to change to floats to handle Psychopy colors
fontName::String = "",
fontSize::Int64 = 12,
scale::Float64 = 1.0,
font::Any = nothing, # font is for internal use and is a pointer to a TTF
horizAlignment::Int64 = -1,
vertAlignment::Int64 = +1,
style::String = "normal",
orientation::Int64 = 0
)
if fontName == ""
font = win.font
else
println("*** Notice: have not implemented loading from system fonts yet")
end
color = colorToSDL(win, color)
new(win,
textMessage ,
pos,
color,
fontName,
fontSize,
scale,
font, # these will need to change to floats to handle Psychopy colors
horizAlignment,
vertAlignment,
style,
orientation
)
end
end
#----------
| PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | code | 747 | export startTimer, stopTimer
"""
startTimer(win::Window)
Starts a timer. Only one timer can run at a time. If you need more than tha one timer, use Julia's time() function.
**Inputs:**
* win::Window
* waitTime::Float64 *default is milliseconds*
**Outputs:** nothing
"""
function startTimer(win::Window)
win.startTime = time()
end
"""
stopTimer(win::Window)
Stops the global timer and returns the time taken. If you need more than one timer, use Julia's time() function.
**Inputs:**
* win::Window
**Outputs:**
The time in [default] milliseconds.
"""
function stopTimer(win::Window)
stopTime = time()
if win.timeScale == "milliseconds"
return (stopTime - win.startTime)*1000.0
else
return (stopTime - win.startTime)
end
end | PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | code | 12822 | # Translation of psycopy window file to Julia
export Window, closeAndQuitPsychoJL, flip, closeWinOnly, hideWindow, getPos, getSize, setFullScreen
export mouseVisible
#
int(x) = floor(Int, x) # for typecasting floats to ints when indexing
"""
Window()
Constructor for a Window object
**Constructor inputs:**
* size::MVector{2, Int64}
* fullScreen::Bool
**Optional constructor inputs:**
* color::MVector{3, Int64}
* colorSpace::String .......*Future. Not implemented yet*
* pos::MVector{2, Float64} ......*position*
* timeScale::String .......*default = "milliseconds"*
* title::String ......*default = "Window"*
**Full list of fields**
* win::Ptr{SDL_Window}
* size::MVector{2, Int64}
* pos::MVector{2, Int64} ......*position*
* color::MVector{3, Int64}
* colorSpace::String
* coordinateSpace::String ......*placeholder for now*
* renderer::Ptr{SDL_Renderer}
* font::Ptr{SimpleDirectMediaLayer.LibSDL2._TTF_Font}
* boldFont::Ptr{SimpleDirectMediaLayer.LibSDL2._TTF_Font}
* italicFont::Ptr{SimpleDirectMediaLayer.LibSDL2._TTF_Font}
* event::Base.RefValue{SDL_Event}
* fullScreen::Bool
* timeScale::String .......*defaults is milliseconds. Other option is seconds*
* title::String
* startTime::Float64 .......*global proximy for startTime() and stopTime()*
**Methods:**
* closeAndQuitPsychoJL()
* closeWinOnly()
* flip()
* getPos()
* getSize()
* hideWindow()
* mouseVisible()
* setFullScreen()
"""
mutable struct Window #{T}
win::Ptr{SDL_Window}
size::MVector{2, Int64} # window size; static array (stay away from tuples)
pos::MVector{2, Int64} # position
color::MVector{3, Int64} # these will be Psychopy colors
colorSpace::String # rgb255, rgba255, decimal, PsychoPy
coordinateSpace::String # LT_Pix, LT_Percent, LB_Percent, PsychoPy
renderer::Ptr{SDL_Renderer}
font::Ptr{SimpleDirectMediaLayer.LibSDL2._TTF_Font}
boldFont::Ptr{SimpleDirectMediaLayer.LibSDL2._TTF_Font}
italicFont::Ptr{SimpleDirectMediaLayer.LibSDL2._TTF_Font}
event::Base.RefValue{SDL_Event} #SDL_Event
fullScreen::Bool
timeScale::String
title::String
startTime::Float64
firstKey::Bool # used for debouncing first keypress
#----------
function Window(size, # window size; static array (stay away from tuples)
fullScreen = false;
color = fill(0, (3)), # these will be Psychopy colors
colorSpace = "rgba255", # might need to revist for colors.jl
coordinateSpace = "LT_Pix",
pos = [SDL_WINDOWPOS_CENTERED,SDL_WINDOWPOS_CENTERED], # position
timeScale = "milliseconds",
title = "Window"
)
winPtr = SDL_CreateWindow(title, SDL_WINDOWPOS_CENTERED, SDL_WINDOWPOS_CENTERED, size[1], size[2], SDL_WINDOW_SHOWN | SDL_WINDOW_ALLOW_HIGHDPI )#| SDL_WINDOW_INPUT_GRABBED)
#winPtr = SDL_CreateWindow(title, SDL_WINDOWPOS_CENTERED, SDL_WINDOWPOS_CENTERED, size[1], size[2], SDL_WINDOW_SHOWN)# | SDL_WINDOW_ALLOW_HIGHDPI )#| SDL_WINDOW_INPUT_GRABBED)
if timeScale != "seconds" && timeScale != "milliseconds"
println("* timeScale can only be 'seconds' or 'milliseconds'.")
println("** ", timeScale, " was given as the value for timeScale.")
println("* default to milliseconds for timing.")
timeScale = "milliseconds"
end
# for default size, try to use a version of the fullscreen size, taking Retina into account
displayInfo = Ref{SDL_DisplayMode}()
SDL_GetCurrentDisplayMode(0, displayInfo)
screenWidth = displayInfo[].w
screenHeight = displayInfo[].h
pos = [screenWidth ÷ 2, screenHeight ÷ 2]
println("screenWidth = ", screenWidth)
println("screenHeight = ", screenHeight)
println("asked for window size = ", size)
SDL_SetHint(SDL_HINT_RENDER_SCALE_QUALITY, "2");
renderer = SDL_CreateRenderer(winPtr, -1, SDL_RENDERER_ACCELERATED | SDL_RENDERER_PRESENTVSYNC)
SDL_SetRenderDrawBlendMode(renderer, SDL_BLENDMODE_BLEND)
baseFilePath = pwd()
baseFilePath =joinpath(baseFilePath,"fonts")
baseFilePath =joinpath(baseFilePath,"Roboto")
fontFilePath =joinpath(baseFilePath,"Roboto-Regular.ttf")
font = TTF_OpenFont(fontFilePath, 30);
if font == C_NULL
if isfile(fontFilePath) == false
error("Could not open file path: " * fontFilePath)
end
error("*** Error: font is NULL")
end
#----------------
# canned BOLD versions look better than asking SDL to bold the font
fontFilePath =joinpath(baseFilePath,"Roboto-Bold.ttf")
boldFont = TTF_OpenFont(fontFilePath, 30);
if boldFont == C_NULL
if isfile(fontFilePath) == false
error("Could not open file path: " * fontFilePath)
end
error("*** Error: font is NULL")
end
#-----------
# canned italic versions look better than asking SDL to bold the font
fontFilePath =joinpath(baseFilePath,"Roboto-Italic.ttf")
italicFont = TTF_OpenFont(fontFilePath, 30);
if italicFont == C_NULL
if isfile(fontFilePath) == false
error("Could not open file path: " * fontFilePath)
end
error("*** Error: font is NULL")
end
#----------------
event = Ref{SDL_Event}()
if fullScreen == true
SDL_SetWindowFullscreen(winPtr, SDL_WINDOW_FULLSCREEN)
end
SDL_PumpEvents() # this erases whatever random stuff was in the backbuffer
SDL_RenderClear(renderer) # <<< Had to do this to clear out the noise.
#---------
firstKey = true
#---------
new(winPtr,
size,
pos,
color,
colorSpace,
coordinateSpace,
renderer,
font,
boldFont,
italicFont,
event,
fullScreen,
timeScale,
title,
firstKey
)
end
end
#----------
"""
closeAndQuitPsychoJL(win::Window)
Attempts to close a PsychoJL Window and quit SDL.
"""
function closeAndQuitPsychoJL(win::Window)
# SDL_DestroyTexture(tex) # this nees to get more complicated, where it loops through a list of textures
println("pre SDL_SetWindowFullscreen")
exit()
SDL_SetWindowFullscreen(win.win, SDL_FALSE)
SDL_DestroyRenderer(win.renderer) # this nees to get more complicated, where it loops through a list of renderers
SDL_DestroyWindow(win.win)
println("pre SDL_Quit")
#SDL_Quit()
exit()
end
#----------
"""
flip(win::Window)
Flips the offscreen buffer on screen. In other words, all of the visual objects that you have drawn offscreen
prior to the flip will now become visible.
"""
function flip(win::Window)
SDL_RenderPresent(win.renderer)
SDL_PumpEvents()
SDL_SetRenderDrawColor(win.renderer, win.color[1], win.color[2], win.color[3], 255)
SDL_RenderClear(win.renderer) # <<< Had to do this to clear out the noise.
end
#----------
"""
closeWinOnly(win::Window)
Attempts to close a PsychoJL Window without quiting SDL.
"""
function closeWinOnly(win::Window)
SDL_DestroyRenderer(win.renderer) # this nees to get more complicated, where it loops through a list of renderers
SDL_DestroyWindow(win.win)
end
#----------
"""
hideWindow(win::Window)
Attempts to hide a PsychoJL Window.
"""
function hideWindow(win::Window)
SDL_HideWindow(win.win)
end
#----------
"""
getPos(win::Window)
Returns the center of the window. This, as well as the dimensions, can chage when going to full screen
"""
function getPos(win::Window)
#=
displayInfo = Ref{SDL_DisplayMode}()
SDL_GetCurrentDisplayMode(0, displayInfo)
screenWidth = displayInfo[].w
screenHeight = displayInfo[].h
=#
w = Ref{Cint}()
h = Ref{Cint}()
SDL_GL_GetDrawableSize(win.win, w, h)
screenWidth = w[]
screenHeight = h[]
win.pos = [screenWidth ÷ 2, screenHeight ÷ 2] # integer division
return win.pos
end
#----------
"""
getSize(win::Window)
Returns the width and height of the window. Dimensions can chage when going to full screen.
"""
function getSize(win::Window)
w = Ref{Cint}()
h = Ref{Cint}()
SDL_GL_GetDrawableSize(win.win, w, h)
screenWidth = w[]
screenHeight = h[]
win.size = [screenWidth, screenHeight ]
return win.size
end
#----------
"""
setFullScreen(win::Window, mode::Bool)
Allows you to flip between windowed and full-screen mode.
"""
function setFullScreen(win::Window, mode::Bool)
if mode == true
SDL_SetWindowFullscreen(win.win, SDL_WINDOW_FULLSCREEN)
else
SDL_SetWindowFullscreen(win.win, SDL_WINDOW_FULLSCREEN_DESKTOP)
end
end
#----------
"""
mouseVisible(mode::Bool)
Hides or shows the cursor
"""
function mouseVisible(visibility::Bool)
if visibility == true
SDL_ShowCursor(SDL_ENABLE)
else
SDL_ShowCursor(SDL_DISABLE)
end
end
#-===============================================
# /System/Library/Fonts
#=
mutable struct Window #{T}
win::Ptr{SDL_Window}
size::MVector{2, Int64} # window size; static array (stay away from tuples)
pos::MVector{2, Float64} # position
color::MVector{3, Int64} # these will be Psychopy colors
colorSpace::String # might need to revist for colors.jl
renderer::Ptr{SDL_Renderer}
font::Ptr{SimpleDirectMediaLayer.LibSDL2._TTF_Font}
boldFont::Ptr{SimpleDirectMediaLayer.LibSDL2._TTF_Font}
italicFont::Ptr{SimpleDirectMediaLayer.LibSDL2._TTF_Font}
event::Base.RefValue{SDL_Event} #SDL_Event
fullScreen::Bool
timeScale::String
title::String
end
#----------
function window( size, # window size; static array (stay away from tuples)
fullScreen = false;
color = fill(0, (3)), # these will be Psychopy colors
colorSpace = "rgb", # might need to revist for colors.jl
pos = [SDL_WINDOWPOS_CENTERED,SDL_WINDOWPOS_CENTERED], # position
timeScale = "milliseconds",
title = "Window"
)
winPtr = SDL_CreateWindow(title, SDL_WINDOWPOS_CENTERED, SDL_WINDOWPOS_CENTERED, size[1], size[2], SDL_WINDOW_SHOWN | SDL_WINDOW_ALLOW_HIGHDPI )#| SDL_WINDOW_INPUT_GRABBED)
if timeScale != "seconds" || timeScale != "milliseconds"
println("**** timeScale can only be 'seconds' or 'milliseconds'.")
println("****", timeScale, " was given as the value for timeScale.")
println("**** default to milliseconds for timing.")
timeScale = "milliseconds"
end
SDL_SetHint(SDL_HINT_RENDER_SCALE_QUALITY, "2");
renderer = SDL_CreateRenderer(winPtr, -1, SDL_RENDERER_ACCELERATED | SDL_RENDERER_PRESENTVSYNC)
# SDL_SetRenderDrawBlendMode(renderer, SDL_BLENDMODE_BLEND)
baseFilePath = pwd()
baseFilePath =joinpath(baseFilePath,"fonts")
baseFilePath =joinpath(baseFilePath,"Roboto")
fontFilePath =joinpath(baseFilePath,"Roboto-Regular.ttf")
# baseFilePath =joinpath(baseFilePath,"Noto_Serif")
# fontFilePath =joinpath(baseFilePath,"NotoSerif-VariableFont_wdth,wght.ttf")
# font = TTF_OpenFont("/Users/MattPetersonsAccount/Documents/Development/Julia/PsychoJL/sans.ttf", 24);
font = TTF_OpenFont(fontFilePath, 30);
if font == C_NULL
if isfile(fontFilePath) == false
error("Could not open file path: " * fontFilePath)
end
error("*** Error: font is NULL")
end
#----------------
# canned BOLD versions look better than asking SDL to bold the font
fontFilePath =joinpath(baseFilePath,"Roboto-Bold.ttf")
boldFont = TTF_OpenFont(fontFilePath, 30);
if boldFont == C_NULL
if isfile(fontFilePath) == false
error("Could not open file path: " * fontFilePath)
end
error("*** Error: font is NULL")
end
#-----------
# canned italic versions look better than asking SDL to bold the font
fontFilePath =joinpath(baseFilePath,"Roboto-Italic.ttf")
italicFont = TTF_OpenFont(fontFilePath, 30);
if italicFont == C_NULL
if isfile(fontFilePath) == false
error("Could not open file path: " * fontFilePath)
end
error("*** Error: font is NULL")
end
#----------------
event = Ref{SDL_Event}()
winStruct = Window(winPtr,
size,
pos,
color,
colorSpace,
renderer,
font,
boldFont,
italicFont,
event,
fullScreen,
timeScale,
title)
if fullScreen == true
SDL_SetWindowFullscreen(winStruct.win, SDL_WINDOW_FULLSCREEN)
end
SDL_PumpEvents() # this erases whatever random stuff was in the backbuffer
SDL_RenderClear(renderer) # <<< Had to do this to clear out the noise.
return winStruct
end
=#
#=
"""
Window()
Constructor for a Window object
constructor inputs:
* size::MVector{2, Int64}
* fullScreen::Bool
optional constructor inputs:
* color::MVector{3, Int64}
* colorSpace::String # Future. Not implemented yet
* pos::MVector{2, Float64} # position
* timeScale::String # default = "milliseconds",
* title::String # default = "Window"
parameters:
* win::Ptr{SDL_Window}
* size::MVector{2, Int64}
* pos::MVector{2, Float64} # position
* color::MVector{3, Int64} # these will be Psychopy colors
* colorSpace::String # might need to revist for colors.jl
* renderer::Ptr{SDL_Renderer}
* font::Ptr{SimpleDirectMediaLayer.LibSDL2._TTF_Font}
* boldFont::Ptr{SimpleDirectMediaLayer.LibSDL2._TTF_Font}
* italicFont::Ptr{SimpleDirectMediaLayer.LibSDL2._TTF_Font}
* event::Base.RefValue{SDL_Event} #SDL_Event
* fullScreen::Bool
* timeScale::String
* title::String
"""
=# | PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | code | 97 | using PsychExpAPIs
using Test
@testset "PsychExpAPIs.jl" begin
# Write your tests here.
end
| PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | docs | 544 | # PsychExpAPIs
#### or PsychoJL for short
PsychoJL is a module for writing psychology and psychophysics experiments. The general framework
and style is inspired by PsychoPy, but there has been no collaboration with the authors of PsychoPy.
Matt Peterson, 2023-2024
[Click here for the manual](https://mpeters2.github.io/PsychExpAPIs.jl/dev/)
[](https://github.com/mpeters2/PsychoJL.jl/actions/workflows/CI.yml?query=branch%3Amain)
| PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | docs | 4095 | ### Color spaces in PsychoJL
The colorspace for your experiment is specified when you make your window.
For example:
```julia
myWin = Window( [2560, 1440], false, colorSpace = "rgba255")
```
#### Colorspaces
`rgb255` red, green, and blue values from 0 to 255. Alpha (opacity) is assumed to be 255 (100%)
* black = [0,0,0]
* 50% gray = [127, 127, 127]
* white = [255, 255, 255]
`rgba255` red, green, blue, and alpha values from 0 to 255.
* black = [0, 0, 0, 255]
* 50% gray = [127, 127, 127, 255]
* white = [255, 255, 255, 255]
`decimal` red, green, blue, and alpha values from 0.0 to 1.0. 0.0 is black and 1.0 is 100%
* black = [0.0, 0.0, 0.0, 1.0]
* 50% gray = [0.5, 0.5, 0.5, 1.0]
* white = [1.0, 1.0, 1.0, 1.0]
`PsychoPy` red, green, blue, and alpha values from -1.0 to 1.0. A value of 0.0 is gray, and +1.0 is 100%
* black = [-1.0, -1.0, -1.0, +1.0]
* 50% gray = [0.0, 0.0, 0.0, +1.0]
* white = [+1.0, +1.0, +1.0, +1.0]
\
Internally, all of these colors will be translated to rgba255 so that they work with SDL (the cross-platform graphics engine that PsychoJL uses).
##### Color fields
Because of the color conversions, you should not access color fields directly. Internally, the color you set is translated to
an SDL color and saved in another variable, which is the variable used for drawing.
In order to translate (and update!) the color, colors should be set either when making the stimulus or using the `setColor()` function.\
For example, while making a new Textstim:
```julia
myText = TextStim(myWin, "Using a TextStim", [100, 100], color = [255, 255, 128])
```
Example using `setColor()`
```julia
setColor(myText, "red")
```
see [Color setting functions](@ref)
#### Colors in PsychoJL
Shapes and TextStim use PsychoColor as their color Type.
`PsychoColor = Union{String, Vector{Int64}, Vector{Float64}}`
What does that gobbledy-gook mean? It means that the constructors and functions accept strings,
Vectors of Int64 (from 0-255) and Vectors of Float 64 (either -1.0...+1.0, or 0.0...+1.0) as inputs.
You can pass a string, an integer vector, or a floating point vector as a color. Keep in mind that the values you pass must
be legal in the color space. For example, if you set the color space to `rgba255` and try to set the color using a floating
point vector, it will throw an error.\
\
Strings are legal in all cases.
##### When the color space is rgb255 or rgba255...
String inputs will be accepted (see [Colors.jl](https://github.com/JuliaGraphics/Colors.jl/blob/master/src/names_data.jl) for a list of color names).\
\
Integer Vectors with a length of 3 (RGB) or a length of 4 (RGBA) will also be accepted. If the length is 3, alpha (opacity) is assumed to be 255 (100%).
Example:
```julia
newRect = Rect(myWin,
100, # width
100, # height
[200,200], # position
lineColor = "dodgerblue", # strings are kosher
fillColor = [255,128,128] # this works if the window's color space is rgb255 or rgba255
)
draw(newRect) # in PsychoPy this would have been newRect.draw()
```
##### When the color space is decimal or PsychoPy...
String inputs will be accepted (see [Colors.jl](https://github.com/JuliaGraphics/Colors.jl/blob/master/src/names_data.jl) for a list of color names).\
\
Float Vectors need a length of 4 (RGBA). How they are interpreted depends on the color space.
If the color space is `decimal`, a value of 0.0 is considered 'black' (in that color channel), and 0.5 is considered gray (50% in that channel).
On the other hand, if the color space is `PsychoPy`, -1.0 s considered 'black' (in that color channel), 0.0 is considered gray (50% in that channel),
and +1.0 is considered white (100% in that channel).
see [Colorspaces](@ref) for example values.
Example:
```julia
newRect = Rect(myWin,
100, # width
100, # height
[200,200], # position
lineColor = "beige", # strings are kosher
fillColor = [1.0, 0.5, 0.5] # this works if the window's color space is decimal or PsychoPy,
)
draw(newRect) # in PsychoPy this would have been newRect.draw()
```
""" | PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | docs | 2439 | ## Coordinate systems
PsychoJL has several diferent coordinate systems available.
* LT_Pix *left top in pixels*
* LT_Percent *left top in percent of height*
* LB_Percent *left bottom in percent of height*
* PsychoPy *Psychopy-style height units*
---
### LT_Pix
The origin is in the left-top corner, positive y-values go downward, and the units of measure are pixels.
The size of the dimensions are determined by the size of your window. All units are in integers (Int64).
##### Note on fullscreen mode
If you set the draw area of your window to less than the full screen size, then draws in full-screen mode will be truncated to the
dimensions of the window you made. This can be confusing, as the screen can appear all black, but drawing is limited to the
subsection of the screen you specified.
---
### LT_Percent
The origin is in the left-top corner, positive y-values go downward, and the units of measure are percentage of the height.
The height dimension always ranges from 0.0 to 1.0, but width varies depending on the aspect ratio of the window.
In the example below, the aspect ratio is 1.7778:1 (2560 x 1440).
All units are floating point (Float64).
---
### LB_Percent
The origin is in the left-bottom corner, positive y-values go upward, and the units of measure are percentage of the height.
The height dimension always ranges from 0.0 to 1.0, but width varies depending on the aspect ratio of the window.
In the example below, the aspect ratio is 1.7778:1 (2560 x 1440).
All units are floating point (Float64).
---
### Psychopy
The origin is in the middle of the screen, positive y-values go upward, and the units of measure are percentage of the height.
The height dimension always ranges from -0.5 to +0.5, but width varies depending on the aspect ratio of the window.
In the example below, the aspect ratio is 1.7778:1 (2560 x 1440).
All units are floating point (Float64).
---
### https://github.com/mpeters2/PsychoJL.jl/blob/main/docs/src/assets/Psychopy.png
```
docs/src/showcase.md
docs/src/assets/logo.png
ME:
docs/src/Coordinates.md
docs/src/assets/Psychopy.png
```
| PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | docs | 200 | ```@docs
displayMessage( message::String)
happyMessage( message::String)
infoMessage( message::String)
warningMessage( message::String)
errorMessage( message::String)
DlgFromDict(dlgDict::Dict)
```
| PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | docs | 78 | ```@docs
ImageStim
draw(theImageStim::ImageStim; magnification::Float64)
```
| PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | docs | 64 | ```@docs
InitPsychoJL()
waitTime(win::Window, time::Float64)
``` | PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | docs | 73 | ```@docs
getKey(win::Window)
waitKeys(win::Window, waitTime::Float64)
``` | PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | docs | 2745 | ## Setter functions
Setter function are used to set the values of the various/struct objects, and should be
used instead of accessing the fields directly. The reason for not accessing them directly is that
often the data you send to the objects needs to be translated to a different representation.\
\
For example:
* "Red" needs to be translated to [255,0,0,255]
* If you are using PsychoPy coordinatse, the coordinate [-0.6, +0.5] might need to be translated to [100, 0].
### Color setting functions
see [Color spaces in PsychoJL](@ref) and [Colors in PsychoJL](@ref)
`setColor(someObject::stimulusType, color::Union{String, Vector{Int64}, Vector{Float64})`\
* where the stimulusType is textStim or Line
`setLineColor(someObject::stimulusType, color::Union{String, Vector{Int64}, Vector{Float64})`\
* where the stimulusType is Rect, Ellipse, or Circle
`setFillColor(someObject::stimulusType, color::Union{String, Vector{Int64}, Vector{Float64})`\
* where the stimulusType is Rect, Ellipse, or Circle
### Position setting functions
see [Coordinate systems](@ref)
Because coordinates may need to be translated to another coordinate system, you should use the `setPos()` function
to update your stimulus' position. The example code below draws a circle, and updates its position periodically.
Example:
```julia
using PsychExpAPIs
# Moving Ball Exampile
#-=============================
function main()
InitPsychoJL()
# make a new floating window using the PsychoPy coordinate space and and color space
win = Window( [1280, 720], false; colorSpace = "PsychoPy", coordinateSpace = "PsychoPy", timeScale = "seconds") # 2560, 1440 [1000,1000]
myCirc = Circle(win,
[ 0.0, 0.0], # screen center
0.1, # radius is 20% of the screen height
fillColor = [+1.0,-1.0,-1.0, +1.0], # r,g,b, alpha
lineColor = "yellow", # has color names
fill = true)
draw(myCirc) # everything draws into memory
flip(win) # copies to screen
waitTime(win, 0.5) # wait one second
for i in 0:10
x = -.5 + (i*0.1) # move circle to the right by 10% of the height
setPos(myCirc, [x, 0]) # Use setPos() to convert PsychoPy to SDL coordinates
draw(myCirc) # everything draws into memory
flip(win) # copies to screen
waitTime(win, 0.1)
end
closeWinOnly(win)
end
#-===============================================================
main()
``` | PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | docs | 469 | see [Setter functions](@ref)
```@docs
Circle
Ellipse
Line
Polygon
Rect
ShapeStim
```
#### draw(various shape types) - Method
Draws the shape (Line, Rect, Ellipse, TextStim, etc.) into the back buffer.
Example:
```julia
newRect = Rect(myWin,
100, # width
100, # height
[200,200], # position
lineColor = [255,0,0],
fillColor = [255,128,128]
)
draw(newRect) # in PsychoPy this would have been newRect.draw()
```
"""
```@docs
setPos
``` | PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | docs | 29 | ```@docs
SoundStim
play
```
| PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | docs | 64 | ```@docs
TextStim
draw(text::TextStim; wrapLength::Int64)
```
| PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | docs | 579 | ```@docs
startTimer(win::Window)
stopTimer(win::Window)
```
#### Alternative approach
An alterntiave to calling these functions is to use Julia's built-in `time()` function, which returns the current time in seconds.
Example:
```julia
...
draw(myStim) # draw stimulus
flip(win) # flip the window onto the screen
startTime = time() # get the current time
keypressed = getKey(win) # wait for a keypress
stopTime = time() # get the current time
timeTaken = stopTime - startTime
println("It took ", timeTaken * 1000," milliseconds for a keypress.")
```
""" | PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | docs | 235 | ```@docs
Window
closeAndQuitPsychoJL(win::Window)
closeWinOnly(win::Window)
flip(win::Window)
getPos(win::Window)
getSize(win::Window)
hideWindow(win::Window)
mouseVisible(visibility::Bool)
setFullScreen(win::Window, mode::Bool)
```
| PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | docs | 7169 |
# Introduction to PsychoJL
PsychoJL is a module for writing psychology and psychophysics experiments. The general framework
and style is inspired by PsychoPy, but there has been no collaboration with the authors of PsychoPy.
Matt Peterson, 2023-2024
## Manual Outline
```@contents
```
## Overview
PsychoJL is a module for writing psychology experiments. Typically, before a trial begins,
stimuli are drawn offscreen into the video buffer. When it is time to present the stimuli,
the flip() function is called and the offscreen image is displayed.
## Differences between PsychoPy and PsychoJL
The main difference between the two involves how objects are called in Julia. For example, to
make and draw a TextStim, you would write something like this in PsychoPy:
```python
stim = visual.TextStim(win,
'Hello World!',
pos=(0.0, 0.0), # center of the screen
color=(1, 0, 0),
colorSpace='rgb')
TextStim.draw()
```
In Julia, it would look like this:
```julia
stim = TextStim(win,
"Hello World!",
[300, 100], # position
color=(255, 0, 0))
draw(stim)
```
Notice that Julia does not use the Object.method() syntax of Python. Instead, the stimulus is passed
to the draw() function.
Python: `object.function(param)`\
Julia: `function(object, param)`
Examples:
```python
myImage.setPos( (0.0, 0.0) )
```
```julia
setPos(myImage, [0.0, 0.0]) # assuming you are using PsychoPy coordinates
```
In addition, Julia objects are really structures (data) with a constructor function of the same name.
For example, I can make a new `TextStim` using the `TextStim()` constructor function, and later change
one of its properties using dot notation.
```julia
stim = TextStim(win,
"Hello World!",
[300, 100], # position
color=(255, 0, 0))
stim.textMessage = "Goodbye, world!"
```
## Performance Tips
Julia can be many orders of magnitude faster than Python. My biggest performance tip is, despite their similarities,
do not write Julia programs like you would write a Python program.
##### Global Variables
For example, although Julia can use global variables, the use of global variables (global constants are OK)
[prevents the optimizing compiler from optimizing](https://docs.julialang.org/en/v1/manual/performance-tips/).
Instead, pass around structs containing what would have been written as global variables in a Python program.
The VisualSearchMain.jl example experiment shows this in action. It uses a struct called ExperimentalDesign.
Although the struct definition is in the global scope, an instance of this structure is created in the
function `makeExperimentalDesign()` and passed around from function-to-function.
```julia
mutable struct ExperimentDesign # we'll pass this around instead of globals
numTrials::Int64
trialSS::Vector{Int64} # this holds the combination of SetSize control
trialTP::Vector{Int64} # Target Presence
randomOrder::Vector{Int64} # this will hold the random order in which the trials will be displayed.
end
```
PsychoJL also makes use of this through the Window instance you create. You may have noticed that most PsychoJL functions
require a window to be passed as one of their parameters. For example, `startTimer()` and `stopTimer()` require a Window to be
passed as one of their arguments.
What in the world does timing have to do with a graphical window? Nothing. However, PsychoJL uses it as a struct that can
hold what would have otherwise been a global variable in another language. Calling `startTimer()` causes it to store the
starting time in the Window you passsed to it. Likewise, `stopTimer()` uses the information stored in the Window structure
to calculate the elapsed time.
##### Variable Typing
Like Python, Julia can infer variables' types. However, Julia can be faster when it does not need to infer types. For example,
the parameter for this function is perfectly legal (from a syntactic point of view):
```julia
function fancyMath(myArray)
answer = doSomeStuff(myArray)
return answer
end
```
But, this is even better, because it explicitely states the parameter's type:
```julia
function fancyMath(myArray::Vector{Float64})
answer = doSomeStuff(myArray)
return answer
end
```
As you might have noticed by the documentation, PsychoJL is strongly typed. Future versions, through
multiple-dispatch (i.e. overloading) will be less strict with their types. For example, for the `startPoint`
and `endPoint`, `Line()` requires a vector of two integers. In the future, it will allow vectors of floats. [edit: the future is here!]
##### Integer Division
When dividing variables that should remain integers, Julia's integer division operand `÷` (not `/`!) is
extremely useful. Dividing integers using the standard division operand `\` can return a float. For example:
```julia
julia> x = 255 ÷ 2
127
```
vs
```julia
julia> x = 255 / 2
127.5
```
Integer division truncates. In other situations `round(Int64, x)` might make more sense.
## Usage Rules
1. The function `InitPsychoJL()` just be called before any PsychoJL functions are called.
2. The `Window()` constructor for the main window should be called before using any PsychoJL functions, other than GUI calls.
3. GUI dialog windows should be called before the main `Window` has been made.
4. GUI dialog windows can be callled after the main `Window has` been closed.
5. Do not taunt Happy Fun Ball.
## Example
The function
```julia
using PsychExpAPIs
function DemoWindow()
InitPsychoJL()
myWin = Window( [1000,1000], false) # dimensions, fullscreen = false
newRect = Rect(myWin,
100, # width
100, # height
[200,200], # position
lineColor = [255,0,0],
fillColor = [255,128,128]
)
draw(newRect) # in PsychoPy this would have been newRect.draw()
myText = TextStim(myWin, # window
"Using a textStim", # text
[300, 100], # position
color = [255, 255, 128]
)
draw(myText) # in PsychoPy this would have been myText.draw()
flip(myWin)
wait(2000) # core.wait in Psychopy. Default timeScale (see Window) is in milliseconds.
end
#------
DemoWindow()
```
## Missing Functionality
mouse events\n
timers (timing can be done by using Julia's time() function)\n
pie-wedges\n
## Known issues
### Manual
The manual is a work in progress, and needs reorganization.
### Timescales
The default timescale is `milliseconds`, but `seconds` is also an option.
The timescale used for your experiment is set by passing `milliseconds` or `seconds` as one of the optional
parameters when creating a main window.
### Monitors
There are some issues that need to be worked out when using high-resolution displays suchs Retina displays. Currently, fullscreen mode draws correctly, but when fullscreen = false,
the image is smaller than expected.
## Technology
All graphics and input are handled by SDL.jl. I translated parts of SDL2_gfxPrimitives from
C to Julia, with some code replaced with more efficient algorithms (and sometimes I couldn't figure out the orignal C code!).
| PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 0.1.0 | 3bb03a80c95594883082fd3fe384f0fe86ffb2cf | docs | 319 | Missing Functionality
1) ShapeStim, Polygon need to be fillable.
2) Timescale not implemented
3) Rotations not implemented. Also need to specify the rotation point
4) setPos() for lines
5) Tutorial/Concepts/References side bar
6) Visual Search needs feedback beep
7) Opacity for imageStims
8) Opacity for all shapes
| PsychExpAPIs | https://github.com/mpeters2/PsychExpAPIs.jl.git |
|
[
"MIT"
] | 1.1.2 | b39b905ff0f39236d47a127e0489fe9a699fd9ba | code | 1466 | using Perceptrons
# training a linear perceptron (solving the OR problem)
X_train = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y_train = [1; 1; 1; 0.0]
X_test = [.8 .9; .01 1; .9 0.2; 0.1 0.2]
model = Perceptrons.fit(X_train,Y_train)
Y_pred = Perceptrons.predict(model,X_test)
println("[Perceptron] accuracy : $(acc(Y_train,Y_pred))")
# training a voted perceptron (solving the OR problem)
model = Perceptrons.fit(X_train,Y_train,centralize=true,mode="voted")
Y_pred = Perceptrons.predict(model,X_test)
println("[Voted Perceptron] accuracy : $(acc(Y_train,Y_pred))")
# training a averaged perceptron (solving the OR problem)
model = Perceptrons.fit(X_train,Y_train,centralize=true,mode="averaged")
Y_pred = Perceptrons.predict(model,X_test)
println("[Averaged Perceptron] accuracy : $(acc(Y_train,Y_pred))")
# training a kernel perceptron (solving the XOR problem)
X_train = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y_train = [0.0 ; 1.0; 1.0; 0.0]
X_test = X_train .+ .03 # adding noise
model = Perceptrons.fit(X_train,Y_train,centralize=true,mode="kernel",kernel="rbf",width=.01)
Y_pred = Perceptrons.predict(model,X_test)
println("[Kernel Perceptron] accuracy : $(acc(Y_train,Y_pred))")
# if you want to save your model
Perceptrons.save(model,filename=joinpath(homedir(),"perceptron_model.jld"))
# if you want to load back your model
model = Perceptrons.load(filename=joinpath(homedir(),"perceptron_model.jld"))
| Perceptrons | https://github.com/lalvim/Perceptrons.jl.git |
|
[
"MIT"
] | 1.1.2 | b39b905ff0f39236d47a127e0489fe9a699fd9ba | code | 3181 | module Perceptrons
using JLD
include("utils.jl")
include("types.jl")
include("linear_perceptron.jl")
include("kernel_perceptron.jl")
include("voted_perceptron.jl")
include("averaged_perceptron.jl")
"""
fit(X::Matrix{:<AbstractFloat},Y::AbstractArray{:<AbstractFloat}; copydata::Bool=true, centralize::Bool=true, kernel="linear", width=1.0, alpha=1.0e-2, shuffle_epoch = true, random_state = true, max_epochs = 5, mode = "linear" )
Perceptron algorithm.
# Arguments
- `copydata::Bool = true`: If you want to use the same input matrix or a copy.
- `centralize::Bool = true`: If you want to z-score columns. Recommended if not z-scored yet.
- `kernel::AbstractString = "rbf"`: If you want to apply a nonlinear Perceptron with gaussian Kernel.
- `width::AbstractFloat = 1.0`: Rbf Kernel width (Only if kernel="rbf").
- `alpha::Real = 1.0e-2`: learning rate.
- `shuffle_epoch::Bool = true`: Shuffle dataset for each epoch. Improves convergency.
- `random_state::Int = 42`: Use a seed to force same results trhough the same dataset.
- `max_epochs::Int = 5`: Maximum epochs.
- `mode::String = "linear"`: modes are "linear", "kernel", "voted" and "averaged" perceptron.
"""
function fit(X::AbstractArray{T},
Y::AbstractArray{T};
copydata::Bool = true,
centralize::Bool = true,
kernel::String = "linear",
width::AbstractFloat = 1.0,
alpha::AbstractFloat = 1.0e-2,
shuffle_epoch::Bool = true,
random_state::Int = 42,
max_epochs::Int = 50,
mode = "linear"
) where T<:AbstractFloat
X = X[:,:]
check_constant_cols(X)
check_constant_cols(Y)
check_params(kernel,mode)
check_data(X, Y)
Xi = (copydata ? deepcopy(X) : X)
Yi = (copydata ? deepcopy(Y) : Y)
check_linear_binary_labels(Yi)
model = Model(X,
alpha,
shuffle_epoch,
random_state,
max_epochs,
centralize,
kernel,
width,
mode)
Xi = (centralize ? centralize_data(Xi,model.mx,model.sx) : Xi)
model.centralize = ( centralize ? true : false )
trainer(model,Xi,Yi)
return model
end
"""
predict(model::Perceptron.Model; X::AbstractArray{:<AbstractFloat}; copydata::Bool=true)
A Perceptron predictor.
# Arguments
- `copydata::Bool = true`: If you want to use the same input matrix or a copy.
"""
function predict(model::PerceptronModel{T},
X::AbstractArray{T};
copydata::Bool=true) where T<:AbstractFloat
X = X[:,:]
check_data(X,model.nfeatures)
Xi = (copydata ? deepcopy(X) : X)
Xi = (model.centralize ? centralize_data(Xi,model.mx,model.sx) : Xi)
Yi = predictor(model,Xi)
return Yi
end
dir(path...) = joinpath(dirname(dirname(@__FILE__)),path...)
end
| Perceptrons | https://github.com/lalvim/Perceptrons.jl.git |
|
[
"MIT"
] | 1.1.2 | b39b905ff0f39236d47a127e0489fe9a699fd9ba | code | 1752 | import Random
function trainer(model::AveragedPerceptron{T},
X::AbstractArray{T},
Y::Vector{T}) where T<:AbstractFloat
shuffle_epoch = model.shuffle_epoch
random_state = model.random_state
max_epochs = model.max_epochs
if random_state!=-1
Random.seed!(random_state)
end
n,m = size(X)
X = hcat(X,ones(n,1)) # adding bias
history = []
nerrors,nlast_errors = Inf,0
epochs = 0
Θ,α = Random.rand(m+1),model.α
step = float(n*max_epochs)
#while nerrors>0 && epochs < max_epochs
while epochs < max_epochs
# stops when error is equal to zero or grater than last_error or reached max iterations
# shuffle dataset
if shuffle_epoch
sind = Random.shuffle(1:n)
x = X[sind,:]
y = Y[sind]
end
nerrors = 0
# weight updates for all samples
for i=1:n
xi = x[i,:]
ξ = sinal(Θ'*xi) - y[i]
if ξ!=0
nerrors+=1
Θ = Θ - (step/(n*max_epochs))* α * ξ * xi
end
step = step - 1
end
nlast_errors = nerrors
epochs+=1
push!(history,nerrors)
end
if nerrors > 0
warn("Perceptron: Not converged. Max epochs $(max_epochs) reached. Error history: $(history) \n Try to increase max_epochs or may be you have a non linear problem.")
end
model.Θ = Θ
model.history = history
end
function predictor(model::AveragedPerceptron{T},
X::AbstractArray{T}) where T<:AbstractFloat
Θ = model.Θ
α = model.α
n = size(X,1)
y = zeros(Real,n)
X = hcat(X,ones(n,1)) # adding bias
for i=1:n
y[i] = sinal(Θ'*X[i,:])
end
y
end
| Perceptrons | https://github.com/lalvim/Perceptrons.jl.git |
|
[
"MIT"
] | 1.1.2 | b39b905ff0f39236d47a127e0489fe9a699fd9ba | code | 2896 |
# A gaussian kernel function
@inline function Φ(x::Vector{T},
y::Vector{T},
r::T=1.0) where T<:AbstractFloat
n = 1.0 / sqrt(2π*r)
s = 1.0 / (2r^2)
return n*exp(-s*sum((x.-y).^2))
end
# A kernel matrix
function ΦΦ(X::AbstractArray{T},
r::T=1.0) where T<:AbstractFloat
n = size(X,1)
K = zeros(n,n)
for i=1:n
for j=1:i
K[i, j] = Φ(X[i, :], X[j, :],r)
K[j, i] = K[i, j]
end
K[i, i] = Φ(X[i, :], X[i, :],r)
end
K
end
# A kernel matrix for test data
function ΦΦ(X::AbstractArray{T},
Z::AbstractArray{T},
r::T=1.0) where T<:AbstractFloat
(nx,mx) = size(X)
(nz,mz) = size(Z)
K = zeros(T,nz, nx)
for i=1:nz
for j=1:nx
K[i, j] = Φ(Z[i, :], X[j, :],r)
end
end
K
end
@inline ∑(λ,y,n,K) = sum(λ .* y .* K)
function trainer(model::KernelPerceptron{T},
X::AbstractArray{T},
Y::Vector{T}) where T<:AbstractFloat
Y[Y .== 0] .= -1 # fix in the future outside this function
max_epochs = model.max_epochs
λ = model.λ # langrange multipliers
K = ΦΦ(X,model.width) # computing the kernel gram matrix
n = size(X,1)
history = []
nerrors = Inf
epochs = 0
while nerrors>0 && epochs < max_epochs
# stops when error is equal to zero or grater than last_error or reached max iterations
nerrors = 0
# weight updates for all samples
for i=1:n
yp = sign(∑(λ,Y,n,K[:,i]))
if Y[i] != yp
nerrors +=1
λ[i] += 1 # missclassification counter for sample i
end
end
epochs+=1
push!(history,nerrors)
end
if nerrors > 0
warn("[Kernel Perceptron] Train not converged. Max epochs $(max_epochs) reached. Error history: $(history) \n Try to increase max_epochs or change kernel params.")
end
# storing only the tough samples ("support vectors")
sv = λ .> 0
model.λ = λ[sv]
model.sv_x = vec(X[sv,:])
model.sv_y = Y[sv]
model.history = history
model.last_epoch = epochs
#println("[Kernel perceptron] #$(length(model.λ)) support vectors out of $(n) samples.")
end
function predictor(model::KernelPerceptron{T},
X::AbstractArray{T}) where T<:AbstractFloat
width = model.width
sv_x,sv_y,λ = model.sv_x,model.sv_y,model.λ
k = size(sv_y,1)
n = size(X,1)
y = zeros(T,n)
for i=1:n
s = .0
for j=1:k # can be vectorized in the future.
s += λ[j] * sv_y[j] * Φ(X[i,:],sv_x[j,:],width) # this is simply a weighted voting into a kernel space
end
y[i] = s
end
y = sign.(y)
y[y .== -1] .= 0 # fix in the future outside this function!!
return y
end
| Perceptrons | https://github.com/lalvim/Perceptrons.jl.git |
|
[
"MIT"
] | 1.1.2 | b39b905ff0f39236d47a127e0489fe9a699fd9ba | code | 1741 | # use in linear perceptron
@inline h(Θ,x) = sinal(Θ'*x)
import Random
function trainer(model::LinearPerceptron{T},
X::AbstractArray{T},
Y::Vector{T}) where T<:AbstractFloat
shuffle_epoch = model.shuffle_epoch
random_state = model.random_state
max_epochs = model.max_epochs
if random_state!=-1
Random.seed!(random_state)
end
n,m = size(X)
X = hcat(X,ones(n,1)) # adding bias
history = []
nerrors,nlast_errors = Inf,0
epochs = 0
Θ = Random.rand(m+1) # already with bias
α = model.α # learning rate
while nerrors>0 && epochs < max_epochs
# stops when error is equal to zero or grater than last_error or reached max iterations
# shuffle dataset
if shuffle_epoch
sind = Random.shuffle(1:n)
x = X[sind,:]
y = Y[sind]
end
nerrors = 0
# weight updates for all samples
for i=1:n
xi = x[i,:]
ξ = h(Θ,xi) - y[i]
if ξ!=0
nerrors+=1
Θ = Θ - α * ξ * xi
end
end
nlast_errors = nerrors
epochs+=1
push!(history,nerrors)
end
if nerrors > 0
warn("Perceptron: Not converged. Max epochs $(max_epochs) reached. Error history: $(history) \n Try to increase max_epochs or may be you have a non linear problem.")
end
model.Θ = Θ
model.α = α
model.history = history
end
function predictor(model::LinearPerceptron{T},
X::AbstractArray{T}) where T<:AbstractFloat
Θ = model.Θ
α = model.α
n,m = size(X)
y = zeros(Real,n)
X = hcat(X,ones(n,1)) # adding bias
for i=1:n
y[i] = h(Θ,X[i,:])
end
y
end
| Perceptrons | https://github.com/lalvim/Perceptrons.jl.git |
|
[
"MIT"
] | 1.1.2 | b39b905ff0f39236d47a127e0489fe9a699fd9ba | code | 7604 | #### Constants
const MODEL_FILENAME = "perceptron_model.jld" # jld filename for storing the model
const MODEL_ID = "perceptron_model" # if od the model in the filesystem jld data
using Statistics
#### An abstract perceptron model
abstract type PerceptronModel{T} end
#### Linear Perceptron type
mutable struct LinearPerceptron{T<:AbstractFloat} <: PerceptronModel{T}
α::T
Θ::Vector{T}
shuffle_epoch::Bool
random_state::Integer
max_epochs::Integer
last_epoch::Integer
history::Vector{Integer}
mx::Matrix{T} # mean stat after for z-scoring input data (X)
sx::Matrix{T} # standard deviation stat after for z-scoring target data (X)
centralize::Bool
nfeatures::Integer
end
function LinearPerceptron(X::AbstractArray{T},
alpha,
shuffle_epoch,
random_state,
max_epochs,
centralize) where T<:AbstractFloat
return LinearPerceptron(alpha, # I will refactor to a constructor. Cleaner
Vector{T}(undef,1),
shuffle_epoch,
random_state,
max_epochs,
0,
Vector{Integer}(undef,1),
mean(X,dims=1),
std(X,dims=1),
centralize,
size(X,2))
end
####################################################################################
#### Linear Perceptron type
mutable struct VotedPerceptron{T<:AbstractFloat} <: PerceptronModel{T}
α::T
Θ#::Dict{Integer,Vector{T}}
c#::Dict{Integer,Integer}
k::Integer
shuffle_epoch::Bool
random_state::Integer
max_epochs::Integer
last_epoch::Integer
history::Vector{Integer}
mx::Matrix{T} # mean stat after for z-scoring input data (X)
sx::Matrix{T} # standard deviation stat after for z-scoring target data (X)
centralize::Bool
nfeatures::Integer
end
function VotedPerceptron(X::AbstractArray{T},
alpha,
shuffle_epoch,
random_state,
max_epochs,
centralize) where T<:AbstractFloat
return VotedPerceptron(alpha, # I will refactor to a constructor. Cleaner
nothing,
nothing,
0,
shuffle_epoch,
random_state,
max_epochs,
0,
Vector{Integer}(undef,1),
mean(X,dims=1),
std(X,dims=1),
centralize,
size(X,2))
end
####################################################################################
#### Kernel Perceptron type
mutable struct KernelPerceptron{T<:AbstractFloat} <: PerceptronModel{T}
λ::Vector{T} # lagrange vector
max_epochs::Integer
last_epoch::Integer
history::Vector{Integer}
mx::Matrix{T} # mean stat after for z-scoring input data (X)
sx::Matrix{T} # standard deviation stat after for z-scoring target data (X)
centralize::Bool
nfeatures::Integer
kernel::String
width::T
sv_x::Vector{T}
sv_y::Vector{T}
end
function KernelPerceptron(X::AbstractArray{T},
max_epochs,
centralize,
kernel,
width) where T<:AbstractFloat
return KernelPerceptron(zeros(T,size(X,1)),
max_epochs,
0,
Vector{Integer}(undef,1),
mean(X,dims=1),
std(X,dims=1),
centralize,
size(X,2),
kernel,
width,
Vector{T}(undef,1),
Vector{T}(undef,1))
end
####################################################################################
#### Averaged Perceptron type
mutable struct AveragedPerceptron{T<:AbstractFloat} <: PerceptronModel{T}
α::T
Θ
shuffle_epoch::Bool
random_state::Integer
max_epochs::Integer
last_epoch::Integer
history::Vector{Integer}
mx::Matrix{T} # mean stat after for z-scoring input data (X)
sx::Matrix{T} # standard deviation stat after for z-scoring target data (X)
centralize::Bool
nfeatures::Integer
end
function AveragedPerceptron(X::AbstractArray{T},
alpha,
shuffle_epoch,
random_state,
max_epochs,
centralize) where T<:AbstractFloat
return AveragedPerceptron(alpha, # I will refactor to a constructor. Cleaner
0,
shuffle_epoch,
random_state,
max_epochs,
0,
Vector{Integer}(undef,1),
mean(X,dims=1),
std(X,dims=1),
centralize,
size(X,2))
end
## choosing types
######################################################################################################
function Model(X,#::AbstractArray{T},
alpha,
shuffle_epoch,
random_state,
max_epochs,
centralize,
kernel,
width,
mode) where T<:AbstractFloat
println("size",size(X))
if mode == "linear"
return LinearPerceptron(X,
alpha,
shuffle_epoch,
random_state,
max_epochs,
centralize)
elseif mode == "kernel"
return KernelPerceptron(X,
max_epochs,
centralize,
kernel,
width)
elseif mode == "voted"
return VotedPerceptron(X,
alpha,
shuffle_epoch,
random_state,
max_epochs,
centralize)
elseif mode == "averaged"
return AveragedPerceptron(X,
alpha,
shuffle_epoch,
random_state,
max_epochs,
centralize)
else
error("Invalid perceptron mode name: $(mode). \n Cadidates are: linear, kernel, voted or averaged")
end
end
######################################################################################################
## Load and Store models (good for production)
function load(; filename::AbstractString = MODEL_FILENAME, modelname::AbstractString = MODEL_ID)
local M
jldopen(filename, "r") do file
M = read(file, modelname)
end
M
end
function save(M::PerceptronModel; filename::AbstractString = MODEL_FILENAME, modelname::AbstractString = MODEL_ID)
jldopen(filename, "w") do file
write(file, modelname, M)
end
end
| Perceptrons | https://github.com/lalvim/Perceptrons.jl.git |
|
[
"MIT"
] | 1.1.2 | b39b905ff0f39236d47a127e0489fe9a699fd9ba | code | 2401 |
## Auxiliary functions
export acc
@inline acc(yt,yp) = count(x->x==true, yt .== yp)/length(yt)
# used in linear and voted perceptron
@inline sinal(x) = ( x>=0 ? 1.0 : 0.0 )
# used in kernel perceptron
@inline sign(val) = ( val >=0 ? 1.0 : -1.0 )
## checks PLS input data and params
function check_data(X::Matrix{T},Y::Union{Vector{T},Matrix{T}}) where T<:AbstractFloat
!isempty(X) ||
throw(DimensionMismatch("Empty input data (X)."))
!isempty(Y) ||
throw(DimensionMismatch("Empty target data (Y)."))
size(X, 1) == size(Y, 1) ||
throw(DimensionMismatch("Incompatible number of rows of input data (X) and target data (Y)."))
end
function check_data(X::Matrix{T},nfeatures::Int) where T<:AbstractFloat
!isempty(X) ||
throw(DimensionMismatch("Empty input data (X)."))
size(X, 2) == nfeatures ||
throw(DimensionMismatch("Incompatible number of columns of input data (X) and original training X columns."))
end
function check_params(kernel::AbstractString,mode::AbstractString)
kernel in ["rbf","linear"] || error("kernel must be 'linear' or 'rbf'")
mode in ["kernel","linear","voted","averaged"] || error("mode must be 'linear' or 'kernel' or 'voted' or 'averaged'")
end
## checks constant columns
check_constant_cols(X::Matrix{T}) where {T<:AbstractFloat} = size(X,1)>1 && !any(all(X .== X[1,:]',dims=1)) || error("You must remove constant columns of input data (X) before train")
check_constant_cols(Y::Vector{T}) where {T<:AbstractFloat} = length(Y)>1 && length(unique(Y)) > 1 || error("Your target values are constant. All values are equal to $(Y[1])")
## Preprocessing data using z-score statistics. this is due to the fact that if X and Y are z-scored, than X'Y returns for W vector a pearson correlation for each element! :)
centralize_data(D::AbstractArray{T}, m::AbstractArray{T}, s::AbstractArray{T}) where {T<:AbstractFloat} = (D .-m)./s
centralize_data(D::Vector{T}, m::T, s::T) where {T<:AbstractFloat} = (D -m)/s
decentralize_data(D::AbstractArray{T}, m::AbstractArray{T}, s::AbstractArray{T}) where {T<:AbstractFloat} = D .*s .+m
decentralize_data(D::Vector{T}, m::T, s::T) where {T<:AbstractFloat} = D *s +m
check_linear_binary_labels(Y::Vector{T}) where {T<:Number} = length(setdiff(Y,[0.,1.]))==0 || error("Your target values must be 1 and 0 only. You have $(unique(Y)) distinct labels")
| Perceptrons | https://github.com/lalvim/Perceptrons.jl.git |
|
[
"MIT"
] | 1.1.2 | b39b905ff0f39236d47a127e0489fe9a699fd9ba | code | 1975 | import Random
@inline function vote(Θ,x,c,k)
s = 0
for j=1:k
s += c[j]*sign(Θ[j]'*x) # voting (+1 or -1 * c[j] weight)
end
s
end
function trainer(model::VotedPerceptron{T},
X::AbstractArray{T},
Y::Vector{T}) where T<:AbstractFloat
shuffle_epoch = model.shuffle_epoch
random_state = model.random_state
max_epochs = model.max_epochs
if random_state!=-1
Random.seed!(random_state)
end
n,m = size(X)
X = hcat(X,ones(n,1)) # adding bias
history = []
nerrors,nlast_errors = Inf,0
epochs = 0
k,Θ,c,α = 1,Dict(1=>Random.rand(m+1)),Dict(1=>0),model.α
#while nerrors>0 && epochs < max_epochs
while epochs < max_epochs
# stops when error is equal to zero or grater than last_error or reached max iterations
# shuffle dataset
if shuffle_epoch
sind = Random.shuffle(1:n)
x = X[sind,:]
y = Y[sind]
end
nerrors = 0
# weight updates for all samples
for i=1:n
xi = x[i,:]
ξ = sinal(Θ[k]'*xi) - y[i]
if ξ==0
c[k] += 1
else
nerrors+=1
c[k+1] = 1
Θ[k+1] = Θ[k] - α * ξ * xi
k += 1
end
end
nlast_errors = nerrors
epochs+=1
push!(history,nerrors)
end
if nerrors > 0
warn("Perceptron: Not converged. Max epochs $(max_epochs) reached. Error history: $(history) \n Try to increase max_epochs or may be you have a non linear problem.")
end
model.Θ = Θ
model.c = c
model.k = k
model.history = history
end
function predictor(model::VotedPerceptron{T},
X::AbstractArray{T}) where T<:AbstractFloat
Θ = model.Θ
α = model.α
k = model.k
c = model.c
n = size(X,1)
y = zeros(Real,n)
X = hcat(X,ones(n,1)) # adding bias
for i=1:n
y[i] = sinal(vote(Θ,X[i,:],c,k))
end
y
end
| Perceptrons | https://github.com/lalvim/Perceptrons.jl.git |
|
[
"MIT"
] | 1.1.2 | b39b905ff0f39236d47a127e0489fe9a699fd9ba | code | 2286 | using Perceptrons
@testset "OR function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 1.0; 1.0; 0.0]
model = Perceptrons.fit(X,Y,centralize=false,mode="averaged",max_epochs=100)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
model = Perceptrons.fit(X,Y,centralize=true,mode="averaged",max_epochs=100)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
end
@testset "Averaged Perceptron Tests (in sample)" begin
@testset "OR function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 1.0; 1.0; 0.0]
model = Perceptrons.fit(X,Y,centralize=false,mode="averaged",max_epochs=100)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
model = Perceptrons.fit(X,Y,centralize=true,mode="averaged",max_epochs=100)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
end
@testset "AND function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 0.0; 0.0; 0.0]
model = Perceptrons.fit(X,Y,centralize=false,mode="averaged",max_epochs=100)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
model = Perceptrons.fit(X,Y,centralize=true,mode="averaged",max_epochs=100)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
end
end
@testset "Averaged Perceptron Tests (out of sample)" begin
@testset "OR function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 1.0; 1.0; 0.0]
Xt = X .+ .3
model = Perceptrons.fit(X,Y,centralize=true,mode="averaged",max_epochs=100)
pred = Perceptrons.predict(model,Xt)
@test all(pred .== Y)
end
#@testset "AND function" begin
# X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
# Y = [1.0 ; 0.0; 0.0; 0.0]
# Xt = X .+ .03
# model = Perceptrons.fit(X,Y,centralize=true,alpha=1.0,mode="averaged",max_epochs=100)
# pred = Perceptrons.predict(model,Xt)
#end
end
@testset "Check Labels" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; -1; 0.0; 0.0]
try
model = Perceptrons.fit(X,Y,mode="averaged",max_epochs=100)
catch
@test true
end
end
| Perceptrons | https://github.com/lalvim/Perceptrons.jl.git |
|
[
"MIT"
] | 1.1.2 | b39b905ff0f39236d47a127e0489fe9a699fd9ba | code | 2702 | using Perceptrons
@testset "Kernel Perceptron Tests (in sample)" begin
@testset "OR function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 1.0; 1.0; 0.0]
model = Perceptrons.fit(X,Y,centralize=false,mode="kernel",kernel="rbf",width=.1)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
model = Perceptrons.fit(X,Y,centralize=true,mode="kernel",kernel="rbf",width=.1)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
end
@testset "AND function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 0.0; 0.0; 0.0]
model = Perceptrons.fit(X,Y,centralize=false,mode="kernel",kernel="rbf",width=.1)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
model = Perceptrons.fit(X,Y,centralize=true,mode="kernel",kernel="rbf",width=.1)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
end
@testset "XOR function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [0.0 ; 1.0; 1.0; 0.0]
model = Perceptrons.fit(X,Y,centralize=false,mode="kernel",kernel="rbf",width=.01)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
model = Perceptrons.fit(X,Y,centralize=true,mode="kernel",kernel="rbf",width=.01)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
end
end
@testset "Kernel Perceptron Tests (out of sample)" begin
@testset "OR function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 1.0; 1.0; 0.0]
Xt = X .+ .3
model = Perceptrons.fit(X,Y,centralize=true,mode="kernel",kernel="rbf",width=.1)
pred = Perceptrons.predict(model,Xt)
@test all(pred .== Y)
end
@testset "AND function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 0.0; 0.0; 0.0]
Xt = X .+ .03
model = Perceptrons.fit(X,Y,centralize=true,mode="kernel",kernel="rbf",width=.1)
pred = Perceptrons.predict(model,Xt)
@test all(pred .== Y)
end
@testset "XOR function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [0.0 ; 1.0; 1.0; 0.0]
Xt = X .+ .03
model = Perceptrons.fit(X,Y,centralize=true,mode="kernel",kernel="rbf",width=.01)
pred = Perceptrons.predict(model,Xt)
@test all(pred .== Y)
end
end
@testset "Check Labels" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; -1; 0.0; 0.0]
try
model = Perceptrons.fit(X,Y,mode="kernel",kernel="rbf",width=1.0)
catch
@test true
end
end
| Perceptrons | https://github.com/lalvim/Perceptrons.jl.git |
|
[
"MIT"
] | 1.1.2 | b39b905ff0f39236d47a127e0489fe9a699fd9ba | code | 1649 | using Perceptrons
@testset "Linear Perceptron Tests (in sample)" begin
@testset "OR function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 1.0; 1.0; 0.0]
model = Perceptrons.fit(X,Y,centralize=false)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
model = Perceptrons.fit(X,Y,centralize=true)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
end
@testset "AND function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 0.0; 0.0; 0.0]
model = Perceptrons.fit(X,Y,centralize=false)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
model = Perceptrons.fit(X,Y,centralize=true)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
end
end
@testset "Linear Perceptron Tests (out of sample)" begin
@testset "OR function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 1.0; 1.0; 0.0]
Xt = X .+ .3
model = Perceptrons.fit(X,Y,centralize=true)
pred = Perceptrons.predict(model,Xt)
@test all(pred .== Y)
end
@testset "AND function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 0.0; 0.0; 0.0]
Xt = X .+ .03
model = Perceptrons.fit(X,Y,centralize=true,alpha=1.0)
pred = Perceptrons.predict(model,Xt)
end
end
@testset "Check Labels" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; -1; 0.0; 0.0]
try
model = Perceptrons.fit(X,Y)
catch
@test true
end
end
| Perceptrons | https://github.com/lalvim/Perceptrons.jl.git |
|
[
"MIT"
] | 1.1.2 | b39b905ff0f39236d47a127e0489fe9a699fd9ba | code | 204 | using Perceptrons
using Test
include("utils_test.jl")
include("linear_perceptron_test.jl")
include("kernel_perceptron_test.jl")
include("voted_perceptron_test.jl")
include("averaged_perceptron_test.jl")
| Perceptrons | https://github.com/lalvim/Perceptrons.jl.git |
|
[
"MIT"
] | 1.1.2 | b39b905ff0f39236d47a127e0489fe9a699fd9ba | code | 1667 | using Statistics
@testset "Auxiliary Functions Test" begin
@testset "check constant columns" begin
try
Perceptrons.check_constant_cols([1.0 1; 1 2;1 3])
catch
@test true
end
try
Perceptrons.check_constant_cols([1.0 1 1][:,:])
catch
@test true
end
try
Perceptrons.check_constant_cols([1.0 2 3][:,:])
catch
@test true
end
try
Perceptrons.check_constant_cols([1.0; 1; 1][:,:])
catch
@test true
end
@test Perceptrons.check_constant_cols([1.0 1;2 2;3 3])
@test Perceptrons.check_constant_cols([1.0;2;3][:,:])
end
@testset "centralize" begin
X = [1; 2 ;3.0][:,:]
X = Perceptrons.centralize_data(X,mean(X,dims=1),std(X,dims=1))
@test all(X .== [-1,0,1.0])
end
@testset "decentralize" begin
Xo = [1; 2; 3.0][:,:]
Xn = [-1,0,1.0][:,:]
Xn = Perceptrons.decentralize_data(Xn,mean(Xo,dims=1),std(Xo,dims=1))
@test all(Xn .== [1; 2; 3.0])
end
@testset "checkparams" begin
try
Perceptrons.check_params("linear")
catch
@test true
end
try
Perceptrons.check_params("x")
catch
@test true
end
end
@testset "checkdata" begin
try
Perceptrons.check_data(zeros(0,0), 0)
catch
@test true
end
try
Perceptrons.check_data(zeros(1,1), 10)
catch
@test true
end
@test Perceptrons.check_data(ones(1,1), 1)
end
@testset "check binary labels" begin
try
Perceptrons.check_linear_binary_labels([1,0,2])
catch
@test true
end
try
Perceptrons.check_linear_binary_labels([1,-1])
catch
@test true
end
@test Perceptrons.check_linear_binary_labels([1,0])
end
end;
| Perceptrons | https://github.com/lalvim/Perceptrons.jl.git |
|
[
"MIT"
] | 1.1.2 | b39b905ff0f39236d47a127e0489fe9a699fd9ba | code | 2246 | using Perceptrons
@testset "OR function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 1.0; 1.0; 0.0]
model = Perceptrons.fit(X,Y,centralize=false,mode="voted",max_epochs=100)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
model = Perceptrons.fit(X,Y,centralize=true,mode="voted",max_epochs=100)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
end
@testset "Voted Perceptron Tests (in sample)" begin
@testset "OR function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 1.0; 1.0; 0.0]
model = Perceptrons.fit(X,Y,centralize=false,mode="voted",max_epochs=100)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
model = Perceptrons.fit(X,Y,centralize=true,mode="voted",max_epochs=100)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
end
@testset "AND function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 0.0; 0.0; 0.0]
model = Perceptrons.fit(X,Y,centralize=false,mode="voted",max_epochs=100)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
model = Perceptrons.fit(X,Y,centralize=true,mode="voted",max_epochs=100)
pred = Perceptrons.predict(model,X)
@test all(pred .== Y)
end
end
@testset "Voted Perceptron Tests (out of sample)" begin
@testset "OR function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 1.0; 1.0; 0.0]
Xt = X .+ .3
model = Perceptrons.fit(X,Y,centralize=true,mode="voted",max_epochs=100)
pred = Perceptrons.predict(model,Xt)
@test all(pred .== Y)
end
@testset "AND function" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; 0.0; 0.0; 0.0]
Xt = X .+ .03
model = Perceptrons.fit(X,Y,centralize=true,alpha=1.0,mode="voted",max_epochs=100)
pred = Perceptrons.predict(model,Xt)
end
end
@testset "Check Labels" begin
X = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y = [1.0 ; -1; 0.0; 0.0]
try
model = Perceptrons.fit(X,Y,mode="voted",max_epochs=100)
catch
@test true
end
end
| Perceptrons | https://github.com/lalvim/Perceptrons.jl.git |
|
[
"MIT"
] | 1.1.2 | b39b905ff0f39236d47a127e0489fe9a699fd9ba | docs | 4322 | Perceptrons.jl
======
A package with several types of Perceptron classifiers. Perceptrons are fast classifiers and can be used even for big data. Up to now, this package contains a linear perceptron, voted perceptron and a Kernel perceptron for binary classification problems. This project will have the following perceptron classifiers: Multiclass, Kernel, Structured, Voted, Average and Sparse. Some state-of-the-art must be included after these.
[](https://travis-ci.org/lalvim/Perceptrons.jl)
[](https://coveralls.io/github/lalvim/Perceptrons.jl?branch=master)
[](http://codecov.io/github/lalvim/Perceptrons.jl?branch=master)
Install
=======
Pkg.add("Perceptrons")
Using
=====
using Perceptrons
Examples
========
using Perceptrons
# training a linear perceptron (solving the OR problem)
X_train = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y_train = [1; 1; 1; 0.0]
X_test = [.8 .9; .01 1; .9 0.2; 0.1 0.2]
model = Perceptrons.fit(X_train,Y_train)
Y_pred = Perceptrons.predict(model,X_test)
println("[Perceptron] accuracy : $(acc(Y_train,Y_pred))")
# training a voted perceptron (solving the OR problem)
model = Perceptrons.fit(X_train,Y_train,centralize=true,mode="voted")
Y_pred = Perceptrons.predict(model,X_test)
println("[Voted Perceptron] accuracy : $(acc(Y_train,Y_pred))")
# training a averaged perceptron (solving the OR problem)
model = Perceptrons.fit(X_train,Y_train,centralize=true,mode="averaged")
Y_pred = Perceptrons.predict(model,X_test)
println("[Averaged Perceptron] accuracy : $(acc(Y_train,Y_pred))")
# training a kernel perceptron (solving the XOR problem)
X_train = [1.0 1.0; 0.0 1.0; 1.0 0.0; 0.0 0.0]
Y_train = [0.0 ; 1.0; 1.0; 0.0]
X_test = X_train .+ .03 # adding noise
model = Perceptrons.fit(X_train,Y_train,centralize=true,mode="kernel",kernel="rbf",width=.01)
Y_pred = Perceptrons.predict(model,X_test)
println("[Kernel Perceptron] accuracy : $(acc(Y_train,Y_pred))")
# if you want to save your model
Perceptrons.save(model,filename=joinpath(homedir(),"perceptron_model.jld"))
# if you want to load back your model
model = Perceptrons.load(filename=joinpath(homedir(),"perceptron_model.jld"))
What is Implemented
======
* Voted Perceptron
* Averaged Perceptron
* Kernel Perceptron
* Linear Perceptron
What is Upcoming
=======
* Multiclass Perceptron
* Structured Perceptron
* Sparse Perceptron
Method Description
=======
* Perceptrons.fit - learns from input data and its related single target
* X::Matrix{:<AbstractFloat} - A matrix that columns are the features and rows are the samples
* Y::Vector{:<AbstractFloat} - A vector with float values.
* copydata::Bool = true: If you want to use the same input matrix or a copy.
* centralize::Bool = true: If you want to z-score columns. Recommended if not z-scored yet.
* mode::AbstractString = "linear": modes are "linear", "kernel", "voted" and "averaged" perceptron.
* kernel::AbstractString = "rbf": If you want to apply a nonlinear Perceptron with gaussian Kernel.
* width::AbstractFloat = 1.0: Rbf Kernel width (Only if kernel="rbf").
* alpha::Real = 1.0e-2: learning rate.
* shuffle_epoch::Bool = true: Shuffle dataset for each epoch. Improves convergency.
* random_state::Int = 42: Use a seed to force same results trhough the same dataset.
* max_epochs::Int = 5: Maximum epochs.
* Perceptrons.predict - predicts using the learnt model extracted from fit.
* model::Perceptrons.Model - A Perceptron model learnt from fit.
* X::Matrix{:<AbstractFloat} - A matrix that columns are the features and rows are the samples.
* copydata::Bool = true - If you want to use the same input matrix or a copy.
References
=======
TODO
License
=======
The Perceptrons.jl is free software: you can redistribute it and/or modify it under the terms of the MIT "Expat"
License. A copy of this license is provided in ``LICENSE.md``
| Perceptrons | https://github.com/lalvim/Perceptrons.jl.git |
|
[
"MIT"
] | 0.1.1 | 6cd44b55d4a3c30540a40f5de15815073974f5ac | code | 9426 | module PkgBake
using PackageCompiler
using ProgressMeter
using MethodAnalysis
#stdlibs
using Artifacts, Base64, CRC32c, Dates, DelimitedFiles,
Distributed, FileWatching,
InteractiveUtils, LazyArtifacts,
Libdl, LibGit2, LinearAlgebra, Logging,
Markdown, Mmap, Printf, Profile, Random, REPL, Serialization, SHA,
SharedArrays, Sockets, SparseArrays, TOML, Test, Unicode, UUIDs,
ArgTools, Downloads, NetworkOptions, Pkg, Statistics, Tar
const base_stdlibs = [Base, Artifacts, Base64, CRC32c, Dates, DelimitedFiles,
Distributed, FileWatching,
InteractiveUtils, LazyArtifacts,
Libdl, LibGit2, LinearAlgebra, Logging,
Markdown, Mmap, Printf, Profile, Random, REPL, Serialization, SHA,
SharedArrays, Sockets, SparseArrays, TOML, Test, Unicode, UUIDs,
ArgTools, Downloads, NetworkOptions, Pkg, Statistics, Tar]
function get_all_modules()
mods = Module[]
for lib in base_stdlibs
visit(lib) do obj
if isa(obj, Module)
push!(mods, obj)
return true # descend into submodules
end
false # but don't descend into anything else (MethodTables, etc.)
end
end
return vcat(mods, base_stdlibs)
end
const bakeable_libs = get_all_modules()
const __BAKEFILE = "bakefile.jl"
global __PRECOMPILE_CURSOR = 0
global __TRACE_PATH = "" # Avoid getting GC'ed
function __init__()
init_dir()
if !have_trace_compile()
path, io = mktemp(;cleanup=false)
close(io) # we don't need it open
global __TRACE_PATH = path
force_trace_compile(__TRACE_PATH)
end
end
function init_dir()
isempty(DEPOT_PATH) && @error "DEPOT_PATH is empty!"
dir = joinpath(DEPOT_PATH[1],"pkgbake")
!isdir(dir) && mkdir(dir)
return abspath(dir)
end
function init_project_dir(project::String)
project_dict = Pkg.Types.parse_toml(project)
if haskey(project_dict, "uuid")
uuid = project_dict["uuid"]
else
uuid = "UNAMED"
# TODO, need to resolve for v1.x somehow as they don't have UUIDs
end
project_dir = joinpath(init_dir(), uuid)
!isdir(project_dir) && mkdir(project_dir)
end
"""
bake
Add additional precompiled methods to Base and StdLibs that are self contained.
"""
function bake(;project=dirname(Base.active_project()), yes=false, useproject=false, replace_default=true)
pkgbakedir = init_dir()
if useproject
add_project_runtime_precompiles(project)
end
precompile_lines = readlines(abspath(joinpath(init_dir(), "bakefile.jl")))
unique!(sort!(precompile_lines))
pc_unsanitized = joinpath(pkgbakedir, "pkgbake_unsanitized.jl")
@info "PkgBake: Writing unsanitized precompiles to $pc_unsanitized"
open(pc_unsanitized, "w") do io
for line in precompile_lines
println(io, line)
end
end
original_len = length(precompile_lines)
sanitized_lines = sanitize_precompile(precompile_lines)
sanitized_len = length(sanitized_lines)
pc_sanitized = joinpath(pkgbakedir, "pkgbake_sanitized.jl")
@info "PkgBake: Writing sanitized precompiles to $pc_sanitized"
open(pc_sanitized, "w") do io
for line in sanitized_lines
println(io, line)
end
end
@info "PkgBake: Found $sanitized_len new precompilable methods for Base out of $original_len generated statements"
!yes && println("Make new sysimg? [y/N]:")
if yes || readline() == "y"
@info "PkgBake: Generating sysimage"
PackageCompiler.create_sysimage(; precompile_statements_file=pc_sanitized, replace_default=replace_default)
push_bakefile_back()
end
nothing
end
function add_project_runtime_precompiles(project)
@info "PkgBake: Observing load-time precompile statements for project: $project"
ctx = create_pkg_context(project)
deps = values(Pkg.dependencies(create_pkg_context(project)))
precompile_lines = String[]
progress = Progress(length(deps), 1)
bakefile_io() do io
println(io, pkgbake_stamp())
for dep in deps
next!(progress, showvalues = [(:dep,dep.name), (:statements, length(precompile_lines))])
# skip stdlibs and non-direct deps
# TODO: Not sure if direct_dep means what i think it does
if in(dep.name, string.(bakeable_libs)) || !dep.is_direct_dep
continue
end
pc_temp = tempname()
touch(pc_temp)
cmd = `$(get_julia_cmd()) --project=$dir --startup-file=no --trace-compile=$pc_temp -e $("using $(dep.name)")`
try
run(pipeline(cmd, devnull))
catch err
if isa(err, InterruptException)
@warn "PkgBake: Interrupted by user"
exit()
else
continue
end
end
for l in eachline(pc_temp,keep=true)
write(io, l)
end
rm(pc_temp)
end
end
end
const N_HISTORY = 10
bakefile_n(n) = abspath(joinpath(init_dir(), "bakefile_$(n).jl"))
function push_bakefile_back()
dir = init_dir()
bake = abspath(joinpath(dir, "bakefile.jl"))
isfile(bakefile_n(N_HISTORY)) && rm(bakefile_n(N_HISTORY))
# push back the history stack
for n in (N_HISTORY-1):1
isfile(bakefile_n(n)) && mv(bakefile_n(n), bakefile_n(n+1),force=true)
end
mv(bake, bakefile_n(1),force=true)
touch(bake)
return nothing
end
"""
sanitize_precompile()
Prepares and sanitizes a julia file for precompilation. This removes any non-concrete
methods and anything non-Base or StdLib.
"""
function sanitize_precompile(precompile_lines::Vector{String})
lines = String[]
for line in precompile_lines
# Generally any line with where is non-concrete, so we can skip.
# Symbol is also runtime dependent so skip as well
if isempty(line) || contains(line, '#') || contains(line, "where") || contains(line, "Symbol(")
continue
else
try
if can_precompile(Meta.parse(line))
push!(lines, line)
end
catch err
show(err)
end
end
end
lines
end
"""
can_precompile
Determine if this expr is something we can precompile.
"""
function can_precompile(ex::Expr)
if ex.head !== :call && ex.args[1] !== :precompile
return false
else
return is_bakeable(ex)
end
end
# TODO: Some Base are marked nospecialize, so we should filter these out also
"""
recurse through the call and make sure everything is in Base, Core, or a StdLib
"""
function is_bakeable(ex::Expr)
# handle submodule (this might not be robust)
if ex.head === :. && is_bakeable(ex.args[1])
return true
end
for arg in ex.args
#@show arg, typeof(arg)
if is_bakeable(arg)
continue
else
return false
end
end
return true
end
function is_bakeable(ex::Symbol)
for lib in bakeable_libs
if isdefined(lib, ex)
return true
else
continue
end
end
return false
end
function is_bakeable(ex::QuoteNode)
return is_bakeable(ex.value)
end
function is_bakeable(n::T) where T <: Number
return true
end
function get_julia_cmd()
julia_path = joinpath(Sys.BINDIR, Base.julia_exename())
cmd = `$julia_path --color=yes --startup-file=no`
end
function create_pkg_context(project)
project_toml_path = Pkg.Types.projectfile_path(project)
if project_toml_path === nothing
error("could not find project at $(repr(project))")
end
return Pkg.Types.Context(env=Pkg.Types.EnvCache(project_toml_path))
end
function pkgbake_stamp()
"\n\t#version = $(VERSION); date = $(Dates.now())"
end
function bakefile_io(f)
bake = abspath(joinpath(init_dir(), "bakefile.jl"))
!isfile(bake) && touch(bake)
open(f, bake, "a")
end
function have_trace_compile()
jloptstc = Base.JLOptions().trace_compile
jloptstc == C_NULL && return false
return true
end
structinfo(T) = [(fieldoffset(T,i), fieldname(T,i), fieldtype(T,i)) for i = 1:fieldcount(T)];
trace_compile_path() = unsafe_string(Base.JLOptions().trace_compile)
current_process_sysimage_path() = unsafe_string(Base.JLOptions().image_file)
"""
force_trace_compile(::String)
Force the trace compile to be enabled for the given file.
"""
function force_trace_compile(path::String)
# find trace-compile field offset
trace_compile_offset = 0
for i = 1:fieldcount(Base.JLOptions)
if fieldname(Base.JLOptions, i) === :trace_compile
trace_compile_offset = fieldoffset(Base.JLOptions, i)
break
end
end
unsafe_store!(cglobal(:jl_options, Ptr{UInt8})+trace_compile_offset, pointer(path))
end
"""
atexit hook for caching precompile files
add to .julia/config/startup.jl
```
using PkgBake
atexit(PkgBake.atexit_hook)
```
"""
function atexit_hook()
!have_trace_compile() && return
trace_path = trace_compile_path()
isempty(trace_path) && return
trace_file = open(trace_path, "r")
bakefile_io() do io
println(io, pkgbake_stamp())
for l in eachline(trace_file, keep=true)
write(io, l)
end
end
close(trace_file)
end
end
| PkgBake | https://github.com/sjkelly/PkgBake.jl.git |
|
[
"MIT"
] | 0.1.1 | 6cd44b55d4a3c30540a40f5de15815073974f5ac | code | 110 | using PkgBake
using Test
@testset "options probe" begin
@test PkgBake.have_trace_compile() == true
end
| PkgBake | https://github.com/sjkelly/PkgBake.jl.git |
|
[
"MIT"
] | 0.1.1 | 6cd44b55d4a3c30540a40f5de15815073974f5ac | docs | 5371 | # PkgBake.jl
PkgBake is designed to enable safe and easy speedups of Julia code loading for Package Developers.
It consists of two elements:
- A precompile caching system
- A method sanitiser
## Using
Inside your `.julia/config/startup.jl` add the following:
```julia
import PkgBake
atexit(PkgBake.atexit_hook)
```
PkgBake will enable the `--trace-compile` equivalent automatically for you, and cache the files into `.julia/pkgbake/`.
If you call julia with `--trace-compile`, PkgBake will copy the files at exit.
To "bake" in the new precompiled statements that are exclusive to Base and Stdlibs, run:
```julia
julia> PkgBake.bake()
```
With this, you should notice anywhere from a 5-15% performance improvment, as Base and Stdlib method have been added to the sysimg.
Of course, this still allows you to change projects and such.
## Design and Use
When the Julia sysimage is created, it knows nothing of downstream
package use. PkgBake is a mechanism to provide specific `precompile` statements only for Base
and Stdlibs to save time and stay out of your way. Since the methods added are only in and for Base and
the Stdlibs, this should have little to no effect on development environments.
This is accomplished by "sanitizing" the precompile statements such that only additional
methods targeting Base and the Stdlib are added to the sysimg.
This is mostly a managment layer over Pkg, PackageCompiler, and MethodAnalysis.
There is some possibility to turning `PkgBake` into a general `precompile` database. Right now, this is
just fun hacks with some marginal profit :)
## Design Possibilities
### 1 - Local Cache
The precompile and loading is done locally.
### 2 - Ecosystem Cache
We pregenerate a Base-only precompile file for each julia version. The user will then just need to
pull this file and run. This will work for every published package.
### 3 - Upstream Target
This can be similar to a Linux distro popcon. PkgBake users upload their sanitized precompile files
and the most common precompiled methods get PRed to base.
### 4 - PkgEval Integration
This is similar to 3, except it is run as part of PkgEval on a new release. This might
require PkgEval to run twice.
### Future
Base only methods do not provide a significant speedup, only 2-5% from what has been observed
so far. A possible way forward is to actually manage the trace-compiles _and_ environments.
e.g. `__init__`s take a good deal of time and can be managed by the project tree.
When extracting the trace compiles we organize by project and manage sysimgs.
### Results (so far)
```
^[[Asteve@sjkdsk1:~$ juliarc
(c, typeof(c)) = (Dict{String,Any}(), Dict{String,Any})
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.5.0-beta1.0 (2020-05-28)
_/ |\__'_|_|_|\__'_| |
|__/ |
julia> @time using Plots
5.647230 seconds (7.96 M allocations: 496.850 MiB, 1.25% gc time)
julia> @time scatter!(rand(50))
5.901242 seconds (10.30 M allocations: 534.544 MiB, 4.81% gc time)
julia> ^C
julia>
steve@sjkdsk1:~$ juliarc --trace-compile=`mktemp`
(c, typeof(c)) = (Dict{String,Any}(), Dict{String,Any})
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.5.0-beta1.0 (2020-05-28)
_/ |\__'_|_|_|\__'_| |
|__/ |
julia> @time using Plots
5.627413 seconds (7.96 M allocations: 496.846 MiB, 1.24% gc time)
julia> @time scatter!(rand(50))
6.068422 seconds (10.29 M allocations: 534.059 MiB, 3.97% gc time)
julia> ^C
julia>
steve@sjkdsk1:~$ juliarc
(c, typeof(c)) = (Dict{String,Any}(), Dict{String,Any})
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.5.0-beta1.0 (2020-05-28)
_/ |\__'_|_|_|\__'_| |
|__/ |
julia> PkgBake.bake()
[ Info: PkgBake: Writing unsanitized precompiles to /home/steve/.julia/pkgbake/pkgbake_unsanitized.jl
[ Info: PkgBake: Writing sanitized precompiles to /home/steve/.julia/pkgbake/pkgbake_sanitized.jl
[ Info: PkgBake: Found 156 new precompilable methods for Base out of 577 generated statements
[ Info: PkgBake: Generating sysimage
[ Info: PackageCompiler: creating system image object file, this might take a while...
[ Info: PackageCompiler: default sysimg replaced, restart Julia for the new sysimg to be in effect
julia> ^C
julia>
steve@sjkdsk1:~$ juliarc
(c, typeof(c)) = (Dict{String,Any}(), Dict{String,Any})
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.5.0-beta1.0 (2020-05-28)
_/ |\__'_|_|_|\__'_| |
|__/ |
julia> @time using Plots
5.466470 seconds (7.61 M allocations: 479.033 MiB, 1.98% gc time)
julia> @time scatter!(rand(50))
5.376421 seconds (9.41 M allocations: 488.071 MiB, 2.19% gc time)
```
| PkgBake | https://github.com/sjkelly/PkgBake.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 304 | push!(LOAD_PATH, "../src/")
using Bactos
using Documenter
makedocs(
sitename = "Bactos.jl",
modules = [Bactos],
pages = [
"Home" => "index.md",
"Tutorial" => "tutorial.md",
"Validation" => "checks.md"
]
)
deploydocs(;
repo = "github.com/mastrof/Bactos.jl"
) | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 1284 | using Bactos
using Distributions
using Plots
θs = [π/6, π/4, π/3, π/2, π]
α = cos.(θs)
U = 30.0 # μm/s
τ = 1.0 # s
ω = 1 / τ
nmicrobes = 100
microbes = [
[
Microbe{3}(
id = n, turn_rate = ω,
motility = RunTumble(speed=[U], polar=[θ,-θ])
) for n in 1:nmicrobes
] for θ in θs
]
dt = 0.05 # s
L = 500.0 # μm
models = [
initialise_model(;
microbes = microbes[i],
timestep = dt, extent = L
) for i in eachindex(microbes)
]
nsteps = round(Int, 100τ_run / dt)
adata = [:pos]
adfs = [run!(model, microbe_step!, nsteps; adata)[1] for model in models]
MSD = hcat(msd.(adfs; L=L)...)
begin
t = (1:nsteps).*dt
T = @. τ / (1-α')
s = t ./ T
D = @. U^2*T/3
MSD_theoretical = @. 6D*T * (s - 1 + exp(-s))
logslice = round.(Int, exp10.(range(0,3,length=10)))
plot(
xlab = "Δt / τ",
ylab = "MSD / (Uτ)²",
legend = :bottomright, legendtitle = "1-α",
scale = :log10,
yticks = exp10.(-2:2:2),
xticks = exp10.(-2:2)
)
scatter!(t[logslice,:]./τ, MSD[logslice,:]./(U*τ)^2,
m=:x, ms=6, msw=2, lab=false, lc=axes(α,1)'
)
plot!(t./τ, MSD_theoretical./(U*τ)^2,
lw=2, lab=round.(1 .- α,digits=2)', lc=axes(α,1)'
)
end | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 1703 | using Bactos
using Plots
U = 30.0 # μm/s
τ_run = 1.0 # s
ω = 1 / τ_run # 1/s
Δt = 0.01 # s
extent = 1e4 # μm
n = 200
microbes_runtumble = [
Microbe{3}(id=i,
turn_rate=ω, motility=RunTumble(speed=[U])
)
for i in 1:n
]
microbes_runrev = [
Microbe{3}(id=n+i,
turn_rate=ω, motility=RunReverse(speed_forward=[U])
)
for i in 1:n
]
microbes_runrevflick = [
Microbe{3}(id=2n+i,
turn_rate=ω, motility=RunReverseFlick(speed_forward=[U])
)
for i in 1:n
]
microbes = vcat(
microbes_runtumble, microbes_runrev, microbes_runrevflick
)
model = initialise_model(;
microbes,
extent, periodic = true,
timestep = Δt
)
nsteps = round(Int, 100τ_run / Δt)
adata = [:vel]
adf, = run!(model, microbe_step!, nsteps; adata)
adf_runtumble = filter(:id => id -> model.agents[id].motility isa RunTumble, adf; view=true)
adf_runrev = filter(:id => id -> model.agents[id].motility isa RunReverse, adf; view=true)
adf_runrevflick = filter(:id => id -> model.agents[id].motility isa RunReverseFlick, adf; view=true)
adfs = [adf_runtumble, adf_runrev, adf_runrevflick]
Φ = hcat([autocorrelation(a,:vel) for a in adfs]...)
t = range(0, (nsteps-1)*Δt; step=Δt)
Φ_theoretical = hcat([
exp.(-t ./ τ_run),
exp.(-t ./ (τ_run / 2)),
(1 .- t ./ (2τ_run)) .* exp.(-t ./ τ_run),
]...) # Taktikos et al. 2013 PLoS ONE
plot(
xlims=(0,6τ_run), ylims=(-0.1, 1.05),
xlab="Δt / τ",
ylab="velocity autocorrelation",
)
plot!(t, Φ_theoretical, lw=2, lc=[1 2 3], label=["Run-Tumble" "Run-Reverse" "Run-Reverse-Flick"])
scatter!(t[1:15:end], Φ[1:15:end,:] ./ U^2, m=:x, mc=[1 2 3], label=false)
hline!([0.0], lw=0.8, ls=:dash, lc=:black, lab=false) | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 1467 | using Bactos
using Plots
conc_field(x,y,C,σ,x₀,y₀) = C * exp(-((x-x₀)^2+(y-y₀)^2)/(2σ^2))
function conc_grad(x,y,C,σ,x₀,y₀)
cfield = conc_field(x,y,C,σ,x₀,y₀)
σ² = σ*σ
return [
-(x-x₀)/σ² * cfield,
-(y-y₀)/σ² * cfield
]
end # function
nmicrobes = 10
microbes = [Brumley{2}(id=i) for i in 1:nmicrobes]
dt = 0.1 # s
L = 500.0 # μm
# field properties
C = 0.1 # μM
σ = 20.0 # μm
x₀ = y₀ = L/2 # μm
concentration_field(pos) = conc_field(pos[1], pos[2], C, σ, x₀, y₀)
concentration_gradient(pos) = conc_grad(pos[1], pos[2], C, σ, x₀, y₀)
model_properties = Dict(
:concentration_field => (pos,_) -> concentration_field(pos),
:concentration_gradient => (pos,_) -> concentration_gradient(pos),
:concentration_time_derivative => (_,_) -> 0.0,
:compound_diffusivity => 500.0, # μm²/s
)
model = initialise_model(;
microbes = microbes,
timestep = dt,
extent = L, periodic = false,
model_properties = model_properties
)
my_microbe_step!(microbe, model) = microbe_step!(
microbe, model;
affect! = brumley_affect!,
turnrate = brumley_turnrate
)
adata = [:pos]
nsteps = 1000
adf, = run!(model, my_microbe_step!, nsteps; adata)
traj = vectorize_adf_measurement(adf, :pos)
x = first.(traj)'
y = last.(traj)'
contourf(
0:L/50:L, 0:L/50:L,
(x,y) -> concentration_field((x,y)),
color=:bone, ratio=1
)
plot!(
x, y, lw=0.5,
colorbar=false, legend=false,
xlims=(0,L), ylims=(0,L)
) | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 1884 | using Bactos
using Plots
#== CONCENTRATION FIELD ==#
conc_field(x,y,C₀,∇C) = C₀ + ∇C*x
function conc_grad(x,y,C₀,∇C)
return [∇C, 0.0]
end # function
#== DOMAIN PARAMETERS ==#
Lx, Ly = 1000.0, 500.0 # μm
extent = (Lx, Ly) # μm
periodic = false
#== MICROBE POPULATION ==#
n = 50
microbes_brumley = [
Brumley{2}(id=i, pos=(0,rand()*Ly), chemotactic_precision=1)
for i in 1:n
]
microbes_brown = [
BrownBerg{2}(id=n+i, pos=(0,rand()*Ly))
for i in 1:n
]
microbes = [microbes_brumley; microbes_brown]
#== FIELD PARAMETERS ==#
C₀ = 0.0 # μM
∇C = 0.01 # μM/μm
concentration_field(pos) = conc_field(pos..., C₀, ∇C)
concentration_gradient(pos) = conc_grad(pos..., C₀, ∇C)
#== MODEL SETUP ==#
timestep = 0.1 # s
model_properties = Dict(
:concentration_field => (pos,_) -> concentration_field(pos),
:concentration_gradient => (pos,_) -> concentration_gradient(pos),
:concentration_time_derivative => (_,_) -> 0.0,
:compound_diffusivity => 500.0, # μm²/s
)
model = initialise_model(;
microbes,
timestep,
extent, periodic,
model_properties,
random_positions = false
)
#== RUN! ==#
adata = [:pos]
nsteps = 1000
adf, = run!(model, microbe_step!, nsteps; adata)
#== POST PROCESSING ==#
traj = vectorize_adf_measurement(adf, :pos)
x = first.(traj)'
y = last.(traj)'
#== PLOTTING ==#
lc = [typeof(m) <: Brumley ? 1 : 2 for m in microbes] |> permutedims
for t in axes(x,1)[1:4:end]
contourf(
0:Lx/50:Lx, 0:Ly/50:Ly,
(x,y) -> concentration_field((x,y)),
color=:bone, ratio=1,
xlims=(0,Lx), ylims=(0,Ly),
xlab="x (μm)", ylab="y (μm)",
colorbar_title="C (μM)", levels=100,
)
t₀ = max(1, t-20)
xt = @view x[t₀:t,:]
yt = @view y[t₀:t,:]
plot!(
xt, yt,
lw=0.5, lc=lc,
legend=false,
)
it = lpad(t, 4, '0')
savefig("frame_$it.png")
end | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 2455 | using Bactos
using Plots
θ(a,b) = a>b ? 1.0 : 0.0
function concentration_field(pos, model)
C₀ = model.C₀
C₁ = model.C₁
t₁ = model.t₁
t₂ = model.t₂
dt = model.timestep
t = model.t * dt
concentration_field(t, C₀, C₁, t₁, t₂)
end
concentration_field(t,C₀,C₁,t₁,t₂) = C₀+C₁*θ(t,t₁)*(1-θ(t,t₂))
concentration_gradient(pos, model) = zero.(pos) # not used by Xie
concentration_time_derivative(pos, model) = 0.0 # not used by Xie
motility_fw = RunReverseFlick(motile_state = MotileState(Forward))
motility_bw = RunReverseFlick(motile_state = MotileState(Backward))
microbes = [
XieNoisy{3}(id=1, turn_rate_forward=0, motility=motility_fw),
XieNoisy{3}(id=2, turn_rate_backward=0, motility=motility_bw)
]
timestep = 0.1 # s
extent = 500.0 # μm
C₀ = 0.01 # μM
C₁ = 5.0-C₀ # μM
T = 60.0 # s
t₁ = 20.0 # s
t₂ = 40.0 # s
nsteps = round(Int, T/timestep)
model_properties = Dict(
:compound_diffusivity => 608.0, # μm²/s
:concentration_field => concentration_field,
:concentration_gradient => concentration_gradient,
:concentration_time_derivative => concentration_time_derivative,
:C₀ => C₀,
:C₁ => C₁,
:t₁ => t₁,
:t₂ => t₂,
)
model = initialise_model(;
microbes, timestep,
extent, model_properties
)
β(a) = a.motility.state == Forward ? a.gain_forward : a.gain_backward
state(a::AbstractXie) = max(1 + β(a)*a.state, 0)
adata = [state, :state_m, :state_z]
adf, = run!(model, microbe_step!, model_step!, nsteps; adata)
S = vectorize_adf_measurement(adf, :state)'
m = (vectorize_adf_measurement(adf, :state_m)')[:,1] # take only fw
z = (vectorize_adf_measurement(adf, :state_z)')[:,1] # take only fw
# response vs time for fw and bw modes
begin
_green = palette(:default)[3]
plot()
x = (0:timestep:T) .- t₁
plot!(
x, S,
lw=1.5, lab=["Forward" "Backward"]
)
plot!(ylims=(-0.1,4.5), ylab="Response", xlab="time (s)")
plot!(twinx(),
x, t -> concentration_field(t.+t₁,C₀,C₁,t₁,t₂),
ls=:dash, lw=1.5, lc=_green, lab=false,
tickfontcolor=_green,
ylab="C (μM)", guidefontcolor=_green
)
end
# methylation and dephosphorylation
begin
x = (0:timestep:T) .- t₁
τ_m = microbes[1].adaptation_time_m
τ_z = microbes[1].adaptation_time_z
M = m ./ τ_m
Z = z ./ τ_z
R = M .- Z
plot(
x, [M Z R],
lw=2,
lab=["m/τ_m" "z/τ_z" "m/τ_m - z/τ_z"],
xlab="time (s)"
)
end | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 2634 | using Bactos
using DelimitedFiles
using StaticArrays
using LinearAlgebra
using Plots
# overlap between spheres
isoverlapping(p1, p2, r1, r2) = (norm(p1 .- p2) ≤ r1+r2)
isoverlapping(a, b) = isoverlapping(a.pos, b.pos, a.radius, b.radius)
# draw a circle
function circleShape(x₀,y₀,r,n=500)
θ = LinRange(0, 2π, n)
x₀ .+ r.*sin.(θ), y₀ .+ r.*cos.(θ)
end # function
# Physical parameters
timestep = 0.1 # s
extent = (1000.0, 500.0) # μm
periodic = false
microbe_radius = 0.5 # μm
ω = 1.0 # 1/s
U = 30.0 # μm/s
motility = RunTumble(speed = Degenerate(U))
Drot = 0.1 # rad²/s
n_microbes = 6
# Initialise obstacles (read configuration from file)
obstacle_data = readdlm("phi04_rmin10_Lx1000_Ly500.dat")
bodyrad = obstacle_data[:,1] # μm
max_radius = maximum(bodyrad)
bodypos = [Tuple(obstacle_data[i,2:3]) for i in axes(obstacle_data,1)] # μm
bodies = [
ObstacleSphere(pos, r, glide!) for (r,pos) in zip(bodyrad,bodypos)
]
# Initialise microbes
microbes = [
Microbe{2}(
id=i, pos=Tuple(rand(2).*extent), vel=rand_vel(2).*U,
turn_rate=1.0, radius=0.5,
motility=RunTumble(speed=Degenerate(U)),
rotational_diffusivity=Drot
) for i in 1:n_microbes
]
# Update microbe positions to avoid overlap with obstacles
for m in microbes
while any(map(b -> isoverlapping(m,b), bodies))
m.pos = Tuple(rand(2) .* extent)
end # while
end # for
# Initialise neighbor list
cutoff_radius = 2 * (max_radius + microbe_radius + U*timestep)
neighborlist = init_neighborlist(microbes, bodies, extent, cutoff_radius, periodic)
model_properties = Dict(
:t => 0,
:bodies => bodies,
:neighborlist => neighborlist,
:cfield_params => (C₀, C₁),
:concentration_field => concentration_field,
:concentration_gradient => concentration_gradient
)
model = initialise_model(;
microbes, timestep, extent, periodic, model_properties,
random_positions = false
)
function update_model!(model)
model.t += 1
if model.t % 10 == 0
update_neighborlist!(model)
end
surface_interaction!(model)
end # function
my_model_step!(model) = model_step!(model; update_model!)
adata = [:pos]
adf, = run!(model, microbe_step!, my_model_step!, 2000; adata)
traj = vectorize_adf_measurement(adf, :pos)
x = first.(traj)'
y = last.(traj)'
plot(
xlims=(0,extent[1]), ylims=(0,extent[2]),
palette=:Dark2, legend=false,
bgcolor=:black, grid=false, axis=false,
ratio=1)
for body in bodies
plot!(
circleShape(body.pos..., body.radius),
seriestype=:shape, lw=0, lab=false,
c=:white, fillalpha=0.25,
)
end # for
plot!(x,y) | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 2937 | using Bactos
using DelimitedFiles
using StaticArrays
using LinearAlgebra
using Plots
# overlap between spheres
isoverlapping(p1, p2, r1, r2) = (norm(p1 .- p2) ≤ r1+r2)
isoverlapping(a, b) = isoverlapping(a.pos, b.pos, a.radius, b.radius)
# draw a circle
function circleShape(x₀,y₀,r,n=100)
θ = LinRange(0, 2π, n)
x₀ .+ r.*sin.(θ), y₀ .+ r.*cos.(θ)
end # function
# Physical parameters
timestep = 0.1 # s
extent = (1000.0, 500.0) # μm
periodic = false
n_microbes = 6
# Initialise obstacles (read configuration from file)
obstacle_data = readdlm("phi04_rmin10_Lx1000_Ly500.dat")
bodyrad = obstacle_data[:,1] # μm
max_radius = maximum(bodyrad)
bodypos = [Tuple(obstacle_data[i,2:3]) for i in axes(obstacle_data,1)] # μm
bodies = [
ObstacleSphere(pos, r, glide!) for (r,pos) in zip(bodyrad,bodypos)
]
# Initialise microbes at x=0
microbes = [Brumley{2}(
id=i, pos=(0,rand()*extent[2])) for i in 1:n_microbes
]
# Update microbe positions to avoid overlap with obstacles
for m in microbes
while any(map(b -> isoverlapping(m,b), bodies))
m.pos = (0, rand()*extent[2])
end # while
end # for
# Initialise neighbor list
cutoff_radius = 3 * max_radius
neighborlist = init_neighborlist(microbes, bodies, extent, cutoff_radius, periodic)
# Setup concentration field
C₀=0.0
C₁=10.0
concentration_field(x,y,C₀,C₁,Lx) = C₀+(C₁-C₀)/Lx*x
function concentration_field(pos, model)
C₀, C₁ = model.cfield_params
Lx = model.space.extent[1]
x, y = pos
concentration_field(x,y,C₀,C₁,Lx)
end
function concentration_gradient(pos,model)
C₀, C₁ = model.cfield_params
Lx = model.space.extent[1]
return ((C₁-C₀)/Lx, 0.0)
end
model_properties = Dict(
:bodies => bodies,
:neighborlist => neighborlist,
:cfield_params => (C₀, C₁),
:concentration_field => concentration_field,
:concentration_gradient => concentration_gradient
)
model = initialise_model(;
microbes, timestep, extent, periodic, model_properties,
random_positions = false
)
function update_model!(model)
update_neighborlist!(model)
surface_interaction!(model)
end # function
my_model_step!(model) = model_step!(model; update_model!)
adata = [:pos]
adf, = run!(model, microbe_step!, my_model_step!, 2000; adata)
traj = vectorize_adf_measurement(adf, :pos)
x = first.(traj)'
y = last.(traj)'
plot(
xlims=(0,extent[1]), ylims=(0,extent[2]),
palette=:Dark2, legend=false,
bgcolor=:black, grid=false, axis=false,
colorbar=:bottom, colorbartitle="C (μM)",
ratio=1)
contourf!(
0:extent[1], 0:extent[2],
(x,y) -> concentration_field(x,y,C₀,C₁,extent[1]),
color=:cividis, levels=100
)
for body in bodies
plot!(
circleShape(body.pos..., body.radius),
seriestype=:shape, lw=0, lab=false,
c=:black, fillalpha=0.5,
)
end # for
plot!(x,y, lc=(1:n_microbes)', lw=1.5)
scatter!(x[end:end,:], y[end:end,:], mc=(1:n_microbes)', ms=8, msc=:black) | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 3047 | using Bactos
using Agents: get_spatial_index
using OrdinaryDiffEq: get_du!
using Plots
default(
thickness_scaling = 1.5,
guidefontsize = 12,
tickfontsize = 12,
legendfontsize = 8,
grid = false,
framestyle = :box,
minorticks = true,
tick_direction = :in,
color_palette = :Dark2,
margin = 3.0Plots.mm
)
nmicrobes = 20
microbes = [BrownBerg{1}(id=i) for i in 1:nmicrobes]
extent = 1000.0
spacing = 0.5
xs = range(-2*spacing, extent+2*spacing; step=spacing)
timestep = 0.1
x₀ = extent/2
C = 10.0
σ = 10.0
D = 10.0
β = 0.004
u₀ = @. C * exp(-(xs-x₀)^2 / (2*σ^2))
∇u = zero(u₀) # to be used as storage in model
∂ₜu = zero(u₀) # to be used as storage in model
finitediff!(∇u, u₀, 1/spacing)
function odestep!(du, u, p, t)
β, D, _dx, = p
a = D * _dx * _dx
# diffusion
laplacian!(du, u, a)
# decay
@. du -= β*u
# absorbing walls
du[1] = du[2] = du[end] = du[end-1] = 0.0
end # function
nsteps = round(Int, 500 / timestep)
ode_integrator = initialise_ode(odestep!, u₀, (β, D, 1/spacing);
dtmax = spacing^2/2D,
saveat = (0:nsteps) .* timestep)
function concentration_field(pos,model)
pos_idx = get_spatial_index(pos, model.xmesh, model)
return model.integrator.u[pos_idx]
end # function
function concentration_gradient(pos, model)
pos_idx = get_spatial_index(pos, model.xmesh, model)
return model.∇u[pos_idx]
end # function
function concentration_time_derivative(pos, model)
pos_idx = get_spatial_index(pos, model.xmesh, model)
return model.∂ₜu[pos_idx]
end # function
model_properties = Dict(
:xmesh => xs,
:∇u => ∇u,
:∂ₜu => ∂ₜu,
:concentration_field => concentration_field,
:concentration_gradient => concentration_gradient,
:concentration_time_derivative => concentration_time_derivative
)
model = initialise_model(;
microbes, timestep,
extent, spacing, periodic = false,
ode_integrator,
model_properties
)
@info "initialised model"
adata = [:pos, :state]
u_field(model) = copy(model.integrator.u)
mdata = [u_field]
when = range(0, nsteps; step=round(Int, 5/timestep))
when_model = range(0, nsteps; step=round(Int, 30/timestep))
function update_model!(model)
# update gradient
finitediff!(model.∇u, model.integrator.u, 1/model.space.spacing)
# update time derivative
get_du!(model.∂ₜu, model.integrator)
end # function
my_model_step!(model) = model_step!(model; update_model!)
adf, mdf = run!(
model, microbe_step!, my_model_step!, nsteps;
adata, mdata, when, when_model
)
@info "simulation complete"
linecolors = palette(:plasma, size(mdf,1))
p1 = plot(color_palette = linecolors)
for row in eachrow(mdf)
plot!(p1, xs[3:end-2], row[:u_field][3:end-2], lw=2, lab=false)
end # for
traj = vectorize_adf_measurement(adf, :pos)
p2 = plot(
first.(traj)', when.*timestep, lab=false, lw=0.5,
line_z=when, color=:plasma, colorbar=false
)
plot(p1,p2,xticks=[0,extent/2,extent]) | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 1568 | using Bactos
using Plots
default(
thickness_scaling = 1.5,
guidefontsize = 12,
tickfontsize = 12,
legendfontsize = 8,
grid = false,
framestyle = :box,
minorticks = true,
tick_direction = :in,
color_palette = :Dark2,
margin = 3.0Plots.mm
)
concentration_field(x,C,σ,x₀) = C * exp(-(x-x₀)^2/(2*σ^2))
concentration_gradient(x,C,σ,x₀) = -(x-x₀)/σ^2 * concentration_field(x,C,σ,x₀)
nmicrobes = 10
microbes = [Microbe{1}(id=i) for i in 1:nmicrobes]
extent = 100.0
spacing = 0.2
xs = range(-2*spacing, extent+2*spacing; step=spacing)
timestep = 0.1
x₀ = extent/2
C = 5.0
σ = 3.0
concentration_field(x) = concentration_field(x,C,σ,x₀)
concentration_gradient(x) = concentration_gradient(x,C,σ,x₀)
u₀ = concentration_field.(xs)
function odestep!(du, u, p, t)
D, _dx, = p
a = D * _dx * _dx
laplacian!(du, u, a)
# absorbing walls
du[1] = du[2] = du[end] = du[end-1] = 0.0
end # function
ode_integrator = initialise_ode(odestep!, u₀, (1.0, 1/spacing);
dtmax = spacing^2/2)
model = initialise_model(;
microbes, timestep,
extent, spacing,
ode_integrator
)
u_field(model) = copy(model.integrator.u)
mdata = [u_field]
nsteps = round(Int, 600 / timestep)
when_model = range(0, nsteps; step=round(Int, 30/timestep))
_, mdf = run!(model, microbe_step!, model_step!, nsteps; mdata, when_model)
linecolors = palette(:plasma, size(mdf,1))
plot(color_palette = linecolors)
for row in eachrow(mdf)
plot!(xs[3:end-2], row[:u_field][3:end-2], lw=2, lab=false)
end # for
plot!() | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 2630 | using Bactos
using DelimitedFiles
using LinearAlgebra
using Plots
# overlap between spheres
isoverlapping(p1, p2, r1, r2) = (norm(p1 .- p2) ≤ r1+r2)
isoverlapping(a, b) = isoverlapping(a.pos, b.pos, a.radius, b.radius)
# draw a circle
function circleShape(x₀,y₀,r,n=50)
θ = LinRange(0, 2π, n)
x₀ .+ r.*sin.(θ), y₀ .+ r.*cos.(θ)
end # function
# Physical parameters
timestep = 0.1 # s
extent = (1000.0, 500.0) # μm
periodic = false
n_microbes = 6
# Initialise obstacles (read configuration from file)
obstacle_data = readdlm("phi065_rmin5_Lx1000_Ly500.dat")
bodyrad = obstacle_data[:,1] # μm
max_radius = maximum(bodyrad)
bodypos = [Tuple(obstacle_data[i,2:3]) for i in axes(obstacle_data,1)] # μm
bodies = [
ObstacleSphere(pos, r) for (r,pos) in zip(bodyrad,bodypos)
]
pathfinder = initialise_pathfinder(extent, periodic, 0.5, bodies)
# Initialise microbes at x=0
microbes = [Celani{2}(
id=i, pos=(0,rand()*extent[2])) for i in 1:n_microbes
]
# Update microbe positions to avoid overlap with obstacles
for m in microbes
while any(map(b -> isoverlapping(m,b), bodies))
m.pos = (0, rand()*extent[2])
end # while
end # for
# Setup concentration field
C₀=0.0
C₁=10.0
concentration_field(x,y,C₀,C₁,Lx) = C₀+(C₁-C₀)/Lx*x
function concentration_field(pos, model)
C₀, C₁ = model.cfield_params
Lx = model.space.extent[1]
x, y = pos
concentration_field(x,y,C₀,C₁,Lx)
end
function concentration_gradient(pos,model)
C₀, C₁ = model.cfield_params
Lx = model.space.extent[1]
return ((C₁-C₀)/Lx, 0.0)
end
model_properties = Dict(
:cfield_params => (C₀, C₁),
:concentration_field => concentration_field,
:concentration_gradient => concentration_gradient,
:pathfinder => pathfinder
)
model = initialise_model(;
microbes, timestep, extent, periodic, model_properties,
random_positions = false
)
adata = [:pos]
@time adf, = run!(model, microbe_step!, model_step!, 8000; adata)
traj = vectorize_adf_measurement(adf, :pos)
x = first.(traj)'
y = last.(traj)'
plot(
xlims=(0,extent[1]), ylims=(0,extent[2]),
palette=:Dark2, legend=false,
bgcolor=:black, grid=false, axis=false,
colorbar=:bottom, colorbartitle="C (μM)",
ratio=1)
contourf!(
0:extent[1], 0:extent[2],
(x,y) -> concentration_field(x,y,C₀,C₁,extent[1]),
color=:cividis, levels=100
)
for body in bodies
plot!(
circleShape(body.pos..., body.radius),
seriestype=:shape, lw=0, lab=false,
c=:black, fillalpha=0.5,
)
end # for
plot!(x,y, lc=(1:n_microbes)')
scatter!(x[end:end,:], y[end:end,:], mc=(1:n_microbes)', ms=8, msc=:black) | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 1151 | using Bactos
using Plots
L = 800.0
τ_run = 1.0
ω = 1 / τ_run
U = 30.0
D_rot = 0.02
n = 1
m_rt = [
Microbe{2}(
id=i, vel=rand_vel(2).*U, turn_rate=ω,
motility=RunTumble(speed=Degenerate(U)),
rotational_diffusivity=D_rot
) for i in 1:n
]
m_rr = [
Microbe{2}(
id=n+i, vel=rand_vel(2).*U, turn_rate=ω,
motility=RunReverse(speed=Degenerate(U)),
rotational_diffusivity=D_rot
) for i in 1:n
]
m_rrf = [
Microbe{2}(
id=2n+i, vel=rand_vel(2).*U, turn_rate=ω,
motility=RunReverseFlick(speed=Degenerate(U)),
rotational_diffusivity=D_rot
) for i in 1:n
]
microbes = vcat(m_rt, m_rr, m_rrf)
Δt = τ_run / 10
model = initialise_model(;
microbes = microbes,
timestep = Δt,
extent = L, periodic = false,
)
nsteps = 500
adata = [:pos]
adf, = run!(model, microbe_step!, nsteps; adata)
trajectories = vectorize_adf_measurement(adf, :pos)
x = first.(trajectories)
y = last.(trajectories)
plot(x', y',
lw=0.5,
ticks=false, lims=(0,L),
lab=["Run-Tumble" "Run-Reverse" "Run-Reverse-Flick"],
legend_foreground_color=:white, legendfontsize=5
) | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 732 | using Bactos
using Plots
default(
thickness_scaling = 1.5,
guidefontsize = 12,
tickfontsize = 12,
legendfontsize = 8,
grid = false,
framestyle = :box,
minorticks = true,
tick_direction = :in,
color_palette = :Dark2,
margin = 3.0Plots.mm
)
dt = 0.1
L = 1e6
nmicrobes = 8
microbes = [Microbe{1}(id=i, pos=(L/2,)) for i in 1:nmicrobes]
model = initialise_model(;
microbes = microbes,
timestep = dt,
extent = L, periodic = false,
)
nsteps = 1000
adata = [:pos]
adf, = run!(model, microbe_step!, nsteps; adata)
x = first.(vectorize_adf_measurement(adf, :pos))'
x₀ = x[1:1,:]
Δx = x .- x₀
plot(
(0:nsteps).*dt, Δx,
legend = false,
xlab = "time",
ylab = "position"
) | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 590 | using Bactos
using Plots
L = 50.0
τ_run = 1.0
ω = 1 / τ_run
nmicrobes = 6
microbes = [
Microbe{2}(
id=i, vel=rand_vel(2), turn_rate=ω,
motility=RunTumble()
) for i in 1:nmicrobes
]
model = initialise_model(;
microbes = microbes,
timestep = 1.0,
extent = L, periodic = false,
random_positions = true,
)
nsteps = 200
adata = [:pos]
adf, = run!(model, microbe_step!, nsteps; adata)
trajectories = vectorize_adf_measurement(adf, :pos)
x = first.(trajectories)
y = last.(trajectories)
plot(x', y',
lw=0.5,
lab=false, ticks=false, lims=(0,L)
) | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 883 | module Bactos
using Agents, Agents.Pathfinding
using CellListMap.PeriodicSystems
using Distributions
using LinearAlgebra
using StaticArrays
using Random
using Rotations
using OrdinaryDiffEq: ODEProblem, DEIntegrator, init, Tsit5, step!
using FiniteDifferences: central_fdm
# Core structures
include("distributions.jl")
include("motility.jl")
include("microbes.jl")
# Utility routines
include("utils.jl")
# ABM setup
include("model.jl")
# Bodies & neighbor lists
include("obstacles_spheres.jl")
include("celllistmap.jl")
# Stepping
export run! # from Agents
include("rotations.jl")
include("step_microbes.jl")
include("step_model.jl")
include("finite_differences.jl")
# Chemotaxis models
include("brown-berg.jl")
include("brumley.jl")
include("celani.jl")
include("xie.jl")
# Measurements
include("drift.jl")
include("msd.jl")
include("correlation_functions.jl")
end # module | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 1980 | export BrownBerg, brownberg_affect!, brownberg_turnrate, microbe_step!
"""
BrownBerg{D} <: AbstractMicrobe{D}
Model of chemotactic E.coli from 'Brown and Berg (1974) PNAS'.
Default parameters:
- motility = RunTumble(speed = Degenerate(30.0))
- turn_rate = 1.49 Hz
- state = 0.0 → corresponds to "weighted dPb/dt" in the paper
- rotational_diffusivity = 0.035 rad²/s
- motor_gain = 660 s
- receptor_binding_constant = 100 μM
- adaptation_time = 1 s
- radius = 0 μm
"""
Base.@kwdef mutable struct BrownBerg{D} <: AbstractMicrobe{D}
id::Int
pos::NTuple{D,Float64} = ntuple(zero, D)
motility = RunTumble(speed = Degenerate(30.0))
vel::NTuple{D,Float64} = rand_vel(D, motility) # μm/s
turn_rate::Float64 = 1/0.67 # 1/s
state::Float64 = 0.0 # 1
rotational_diffusivity = 0.035 # rad²/s
motor_gain::Float64 = 660.0 # s
receptor_binding_constant::Float64 = 100.0 # μM
adaptation_time::Float64 = 1.0 # s
radius::Float64 = 0.0 # μm
end # struct
function brownberg_affect!(microbe, model)
Δt = model.timestep
τₘ = microbe.adaptation_time
β = Δt / τₘ # memory loss factor
KD = microbe.receptor_binding_constant
S = microbe.state # weighted dPb/dt at previous step
u = model.concentration_field(microbe.pos, model)
∇u = model.concentration_gradient(microbe.pos, model)
∂ₜu = model.concentration_time_derivative(microbe.pos, model)
du_dt = dot(microbe.vel, ∇u) + ∂ₜu
M = KD / (KD + u)^2 * du_dt # dPb/dt from new measurement
microbe.state = β*M + S*exp(-β) # new weighted dPb/dt
return nothing
end # function
function brownberg_turnrate(microbe, model)
ν₀ = microbe.turn_rate # unbiased
g = microbe.motor_gain
S = microbe.state
return ν₀*exp(-g*S) # modulated turn rate
end # function
function microbe_step!(microbe::BrownBerg, model::ABM)
microbe_step!(
microbe, model;
affect! = brownberg_affect!,
turnrate = brownberg_turnrate
)
end # function | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 2322 | export Brumley, brumley_affect!, brumley_turnrate
"""
Brumley{D} <: AbstractMicrobe{D}
Model of chemotactic bacterium from 'Brumley et al. (2019) PNAS'.
The model is optimized for simulation of marine bacteria and accounts
for the presence of (gaussian) sensing noise in the chemotactic pathway.
Default parameters:
- motility = RunReverseFlick(speed_forward = Degenerate(46.5))
- turn_rate = 2.22 Hz → '1/τ₀'
- state = 0.0 → 'S'
- rotational_diffusivity = 0.035 rad²/S
- adaptation_time = 1.3 s → 'τₘ'
- receptor_gain = 50.0 μM⁻¹ → 'κ'
- motor_gain = 50.0 → 'Γ'
- chemotactic_precision = 6.0 → 'Π'
- radius = 0.5 μm → 'a'
"""
Base.@kwdef mutable struct Brumley{D} <: AbstractMicrobe{D}
id::Int
pos::NTuple{D,Float64} = ntuple(zero, D)
motility = RunReverseFlick(speed_forward = Degenerate(46.5))
vel::NTuple{D,Float64} = rand_vel(D, motility) # μm/s
turn_rate::Float64 = 1/0.45 # 1/s
state::Float64 = 0.0
rotational_diffusivity::Float64 = 0.035 # rad²/s
adaptation_time::Float64 = 1.3 # s
receptor_gain::Float64 = 50.0 # 1/μM
motor_gain::Float64 = 50.0 # 1
chemotactic_precision::Float64 = 6.0 # 1
radius::Float64 = 0.5 # μm
end # struct
function brumley_affect!(microbe, model)
Δt = model.timestep
Dc = model.compound_diffusivity
τₘ = microbe.adaptation_time
α = exp(-Δt/τₘ) # memory persistence factor
a = microbe.radius
Π = microbe.chemotactic_precision
κ = microbe.receptor_gain
u = model.concentration_field(microbe.pos, model)
∇u = model.concentration_gradient(microbe.pos, model)
∂ₜu = model.concentration_time_derivative(microbe.pos, model)
# gradient measurement
μ = dot(microbe.vel, ∇u) + ∂ₜu # mean
σ = Π * 0.04075 * sqrt(3*u / (π*a*Dc*Δt^3)) # noise
M = rand(Normal(μ,σ)) # measurement
# update internal state
S = microbe.state
microbe.state = α*S + (1-α)*κ*τₘ*M
return nothing
end # function
function brumley_turnrate(microbe, model)
ν₀ = microbe.turn_rate # unbiased
Γ = microbe.motor_gain
S = microbe.state
return (1 + exp(-Γ*S)) * ν₀/2 # modulated turn rate
end # function
function microbe_step!(microbe::Brumley, model::ABM)
microbe_step!(
microbe, model;
affect! = brumley_affect!,
turnrate = brumley_turnrate
)
end # function | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 3559 | export
AbstractCelani, Celani, CelaniNoisy,
celani_affect!, celani_turnrate, microbe_step!
abstract type AbstractCelani{D} <: AbstractMicrobe{D} end
"""
Celani{D} <: <: AbstractCelani{D} <: AbstractMicrobe{D}
Model of chemotactic bacterium using the response kernel from 'Celani and Vergassola (2010) PNAS'.
Default parameters:
- motility = RunTumble(speed = Degenerate(30.0))
- turn_rate = 1.49 Hz
- state = zeros(4)
- rotational_diffusivity = 0.26 rad²/s
- gain = 50.0
- memory = 1 s
- radius = 0 μm
"""
Base.@kwdef mutable struct Celani{D} <: AbstractCelani{D}
id::Int
pos::NTuple{D,Float64} = ntuple(zero, D)
motility = RunTumble(speed = Degenerate(30.0))
vel::NTuple{D,Float64} = rand_vel(D, motility) # μm/s
turn_rate::Float64 = 1/0.67 # 1/s
state::Vector{Float64} = [0.,0.,0.,1.] # 1
rotational_diffusivity = 0.26 # rad²/s
gain::Float64 = 50.0 # 1
memory::Float64 = 1.0 # s
radius::Float64 = 0.5 # μm
end # struct
"""
CelaniNoisy{D} <: AbstractCelani{D} <: AbstractMicrobe{D}
Model of chemotactic bacterium using the response kernel from 'Celani and Vergassola (2010) PNAS'
with a custom implementation of noisy sensing based on 'Berg and Purcell (1977) Biophys J'.
The intensity of noise implicit in bacterial sensing is represented by a dimensionless
factor `chemotactic_precision` (same approach used by 'Brumley et al. (2019) PNAS').
`chemotactic_precision = 1` represents the minimum theoretical noise.
Default parameters:
- motility = RunTumble(speed = Degenerate(30.0))
- turn_rate = 1.49 Hz
- state = zeros(4)
- rotational_diffusivity = 0.26 rad²/s
- gain = 50.0
- memory = 1 s
- chemotactic_precision = 1.0
- radius = 0 μm
"""
Base.@kwdef mutable struct CelaniNoisy{D} <: AbstractCelani{D}
id::Int
pos::NTuple{D,Float64} = ntuple(zero, D)
motility = RunTumble(speed = Degenerate(30.0))
vel::NTuple{D,Float64} = rand_vel(D, motility) # μm/s
turn_rate::Float64 = 1/0.67 # 1/s
state::Vector{Float64} = [0.,0.,0.,1.] # 1
rotational_diffusivity = 0.26 # rad²/s
gain::Float64 = 50.0 # 1
memory::Float64 = 1.0 # s
chemotactic_precision::Float64 = 1.0 # 1
radius::Float64 = 0.5 # μm
end # struct
function celani_affect!(microbe::Celani, model)
Δt = model.timestep
u = model.concentration_field(microbe.pos, model)
γ = microbe.memory
λ = 1/γ
β = microbe.gain
S = microbe.state
S[1] = S[1] + (-λ*S[1] + u)*Δt
S[2] = S[2] + (-λ*S[2] + S[1])*Δt
S[3] = S[3] + (-λ*S[3] + 2*S[2])*Δt
S[4] = 1 - β*(λ^2*S[2] - λ^3/2*S[3])
return nothing
end # function
function celani_affect!(microbe::CelaniNoisy, model)
Δt = model.timestep
Dc = model.compound_diffusivity
u = model.concentration_field(microbe.pos, model)
a = microbe.radius
Π = microbe.chemotactic_precision
σ = Π * 0.04075 * sqrt(3*u / (5*π*Dc*a*Δt)) # noise (Berg-Purcell)
M = rand(Normal(u,σ)) # measurement
γ = microbe.memory
λ = 1/γ
β = microbe.gain
S = microbe.state
S[1] = S[1] + (-λ*S[1] + M)*Δt
S[2] = S[2] + (-λ*S[2] + S[1])*Δt
S[3] = S[3] + (-λ*S[3] + 2*S[2])*Δt
S[4] = 1 - β*(λ^2*S[2] - λ^3/2*S[3])
return nothing
end # function
function celani_turnrate(microbe, model)
ν₀ = microbe.turn_rate # unbiased
S = microbe.state[4]
return ν₀*S # modulated turn rate
end # function
function microbe_step!(microbe::AbstractCelani, model::ABM)
microbe_step!(
microbe, model;
affect! = celani_affect!,
turnrate = celani_turnrate
)
end # function | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 4792 | export
init_neighborlist, update_neighborlist!,
surface_interaction!
"""
init_neighborlist(
x::AbstractVector,
extent::Union{<:Real,NTuple{D,<:Real}},
cutoff::Real, periodic::Bool
) where D
Initialise a neighbor list between objects in `x`
in a domain of size `extent` with a neighbor cutoff radius given by `cutoff`.
`periodic` determines whether the system has periodic boundary conditions.
Uses the `PeriodicSystem` interface of `CellListMap`.
"""
function init_neighborlist(
x::AbstractVector,
extent::Real, cutoff::Real, periodic::Bool
)
D = length(getpos(first(x)))
init_neighborlist(x, ntuple(_->extent,D), cutoff, periodic)
end
function init_neighborlist(
x::AbstractVector,
extent::NTuple{D,<:Real}, cutoff::Real, periodic::Bool
) where D
xpos = getpos.(x)
return PeriodicSystem(
xpositions = xpos,
unitcell = SVector(extent) .+ (periodic ? 0.0 : cutoff),
cutoff = cutoff,
output = 0.0
)
end # function
"""
init_neighborlist(
x::AbstractVector, y::AbstractVector,
extent::Union{<:Real,NTuple{D,<:Real}},
cutoff::Real, periodic::Bool
) where D
Initialise a neighbor list between objects in `x` and `y`
in a domain of size `extent` with a neighbor cutoff radius given by `cutoff`.
`periodic` determines whether the system has periodic boundary conditions.
Uses the `PeriodicSystem` interface of `CellListMap`.
"""
function init_neighborlist(
x::AbstractVector, y::AbstractVector,
extent::Real, cutoff::Real, periodic::Bool
)
D = length(getpos(first(x)))
init_neighborlist(x, y, ntuple(_->extent,D), cutoff, periodic)
end
function init_neighborlist(
x::AbstractVector, y::AbstractVector,
extent::NTuple{D,<:Real}, cutoff::Real, periodic::Bool
) where D
xpos = getpos.(x)
ypos = getpos.(y)
return PeriodicSystem(
xpositions = xpos,
ypositions = ypos,
unitcell = SVector(extent) .+ (periodic ? 0.0 : cutoff),
cutoff = cutoff,
output = 0.0
)
end # function
getpos(x::AbstractVector) = SVector{length(x)}(x)
getpos(x::NTuple{D,<:Real}) where D = SVector{D}(x)
getpos(x::AbstractMicrobe{D}) where D = SVector{D}(x.pos)
getpos(x::ObstacleSphere{D}) where D = SVector{D}(x.pos)
"""
update_neighborlist!(model; listname=:neighborlist, x_or_y='x')
Update the position of all microbes in a neighbor list in `model`.
Must be passed in the `update_model!` function to `model_step!`.
## Keywords
* `listname::Symbol = :neighborlist`: name of the neighbor list to update
(`model.properties[listname]`); this is useful if different neighbor lists are used
(e.g. to evaluate different types of interactions).
* `x_or_y::Char = 'x'`: update the `xpositions` or the `ypositions` field in
the neighbor list.
"""
function update_neighborlist!(model::ABM;
listname::Symbol = :neighborlist,
x_or_y::Char = 'x'
)
for microbe in allagents(model)
update_neighborlist!(microbe, model; listname, x_or_y)
end
end
"""
update_neighborlist!(microbe, model; listname=:neighborlist, x_or_y='x')
Update the position of `microbe` in a neighbor list.
Must be passed as the `affect!` function to `microbe_step!`.
## Keywords
* `listname::Symbol = :neighborlist`: name of the neighbor list to update
(`model.properties[listname]`); this is useful if different neighbor lists are used
(e.g. to evaluate different types of interactions).
* `x_or_y::Char = 'x'`: update the `xpositions` or the `ypositions` field in
the neighbor list.
"""
function update_neighborlist!(microbe::AbstractMicrobe, model::ABM;
listname::Symbol = :neighborlist,
x_or_y::Char = 'x'
)
neighborlist = model.properties[listname]
if lowercase(x_or_y) == 'x'
neighborlist.xpositions[microbe.id] = SVector(microbe.pos)
elseif lowercase(x_or_y) == 'y'
neighborlist.ypositions[microbe.id] = SVector(microbe.pos)
else
throw(ArgumentError(
"Value $(x_or_y) not valid for `x_or_y` keyword."
))
end
return nothing
end # function
function surface_interaction!(x,y,i,j,d²,f,model)
body = model.bodies[j]
body.affect!(model[i], body, model)
return f
end # function
"""
surface_interaction!(model; listname=:neighborlist)
Evaluate the effect of surface interactions between microbes and bodies
using the neighborlist for efficient computation.
Requires the neighborlist (initialised via `init_neighborlist`) to be set
as a model property `model.properties[listname]`.
"""
function surface_interaction!(model::ABM; listname::Symbol=:neighborlist)
map_pairwise!(
(x,y,i,j,d²,f) -> surface_interaction!(x,y,i,j,d²,f,model),
model.properties[listname]
)
return nothing
end # function | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 1450 | export autocorrelation
"""
autocorrelation(adf, sym::Union{String,Symbol}; tstep::Int=1)
Return the non-normalized autocorrelation function of quantity `sym` extracted
from the dataframe `adf` (`adf[!,sym]`).
The kwarg `tstep` defines the values of time-lags for sampling (defaults to 1).
"""
function autocorrelation(adf, sym::Union{String,Symbol}; tstep::Int=1)
timeseries = vectorize_adf_measurement(adf, sym)
autocorrelation(timeseries; tstep=tstep)
end # function
function autocorrelation(timeseries::T; tstep::Int=1) where {S,T<:AbstractVector{S}}
nsteps, = size(timeseries)
timelags = range(0, nsteps-2; step=tstep)
f = zeros(nsteps-1)
for (j,Δt) in enumerate(timelags)
for t₀ in 1:nsteps-Δt
u = timeseries[t₀]
v = timeseries[t₀+Δt]
f[j] += dot(u,v)
end # for
f[j] /= (nsteps-j)
end # for
return f
end # function
function autocorrelation(timeseries::T; tstep::Int=1) where {S,T<:AbstractMatrix{S}}
nmicrobes, nsteps = size(timeseries)
timelags = range(0, nsteps-2; step=tstep)
f = zeros(nsteps-1)
for (j,Δt) in enumerate(timelags)
for t₀ in 1:nsteps-Δt
for i in 1:nmicrobes
u = timeseries[i, t₀]
v = timeseries[i, t₀+Δt]
f[j] += dot(u,v)
end # for
end # for
f[j] /= (nmicrobes * (nsteps-j))
end # for
return f
end # function | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 559 | export Degenerate, Arccos
struct Degenerate{T<:Real} <: ContinuousUnivariateDistribution
x::T
end # struct
Base.rand(d::Degenerate) = d.x
struct Arccos{T<:Real} <: ContinuousUnivariateDistribution
a::T
b::T
Arccos{T}(a::T, b::T) where {T} = new{T}(a::T, b::T)
end
function Arccos(a::Real, b::Real; check_args::Bool=true)
Distributions.@check_args Arccos a<b -1≤a≤1 -1≤b≤1
return Arccos{Float64}(Float64(a), Float64(b))
end # function
Arccos() = Arccos(-1,1)
Base.rand(rng::AbstractRNG, d::Arccos) = acos(rand(rng, Uniform(d.a, d.b))) | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 2312 | export driftvelocity_point, driftvelocity_direction
"""
driftvelocity_point(adf, target; normalize=false)
Evaluate the drift velocity of microbes towards a point `target`,
extracting their positions and velocities from the agent dataframe `adf`
(requires the existence of `:pos` and `:vel` fields).
Returns a matrix of instantaneous drift velocities with size
(nmicrobes, nsteps). By convention the drift velocity will be positive
for motion towards the target point.
If `normalize` is set to `true`, drift velocities are normalized by the
instantaneous speed of the microbe.
"""
function driftvelocity_point(adf, target; normalize=false)
traj = vectorize_adf_measurement(adf, :pos)
vels = vectorize_adf_measurement(adf, :vel)
driftvelocity_point(traj, vels, target; normalize=normalize)
end # function
function driftvelocity_point(traj::T, vels::T, target;
normalize=false) where {T<:AbstractMatrix}
v_drift = zeros(size(traj)...)
for k in eachindex(traj)
pos = traj[k]
vel = vels[k]
# axis is the vector from microbe to target
axis = target .- pos
# project velocity onto axis
v_drift[k] = dot(vel, axis) / norm(axis)
if normalize
v_drift[k] /= norm(vel)
end # if
end # for
return v_drift
end # function
"""
driftvelocity_direction(adf, target; normalize=false)
Evaluate the drift velocity of microbes along a direction `target`,
extracting their velocities from the agent dataframe `adf` (requires `:vel`
field).
Returns a matrix of instantaneous drift velocities with size
(nmicrobes, nsteps). By convention the drift velocity will be positive
for motion along the target direction.
If `normalize` is set to `true`, drift velocities are normalized by the
instantaneous speed of the microbe.
"""
function driftvelocity_direction(adf, target; normalize=false)
vels = vectorize_adf_measurement(adf, :vel)
driftvelocity_direction(vels, target; normalize=normalize)
end # function
function driftvelocity_direction(vels::AbstractMatrix, target; normalize=false)
if normalize
v_drift = map(vel -> dot(vel, target) / norm(target) / norm(vel), vels)
else
v_drift = map(vel -> dot(vel, target) / norm(target), vels)
end # if
return v_drift
end # function | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 6411 | export
CFDM_3_1, CFDM_3_2,
finitediff!, laplacian!, divergence!
# pre-computed finite difference stencils
global const CFDM_3_1 = central_fdm(3, 1)
global const CFDM_3_2 = central_fdm(3, 2)
# derivative functions for internal usage
function ∂x(u::AbstractVector{Float64}, i::Int, FDM)
s::Float64 = 0.0
for (q,h) in zip(FDM.grid, FDM.coefs)
s += u[i+q] * h
end # for
return s
end # function
function ∂x(u::AbstractMatrix{Float64}, i::Int, j::Int, FDM)
s::Float64 = 0.0
for (q,h) in zip(FDM.grid, FDM.coefs)
s += u[i+q, j] * h
end # for
return s
end # function
function ∂y(u::AbstractMatrix{Float64}, i::Int, j::Int, FDM)
s::Float64 = 0.0
for (q,h) in zip(FDM.grid, FDM.coefs)
s += u[i, j+q] * h
end # for
return s
end # function
function ∂x(u::AbstractArray{Float64,3}, i::Int, j::Int, k::Int, FDM)
s::Float64 = 0.0
for (q,h) in zip(FDM.grid, FDM.coefs)
s += u[i+q, j, k] * h
end # for
return s
end # function
function ∂y(u::AbstractArray{Float64,3}, i::Int, j::Int, k::Int, FDM)
s::Float64 = 0.0
for (q,h) in zip(FDM.grid, FDM.coefs)
s += u[i, j+q, k] * h
end # for
return s
end # function
function ∂z(u::AbstractArray{Float64,3}, i::Int, j::Int, k::Int, FDM)
s::Float64 = 0.0
for (q,h) in zip(FDM.grid, FDM.coefs)
s += u[i, j, k+q] * h
end # for
return s
end # function
"""
finitediff!(ux, u, a, FDM=CFDM_3_1)
finitediff!(ux, uy, u, ax, ay, FDM=CFDM_3_1)
finitediff!(ux, uy, u, a, FDM=CFDM_3_1)
finitediff!(ux, uy, uz, u, ax, ay, az, FDM=CFDM_3_1)
finitediff!(ux, uy, uz, u, a, FDM=CFDM_3_1)
Evaluate derivative of `u` through the finite difference stencil `FDM`
and store the results in the appropriate arrays.
If `u` has more than one dimension, it is assumed that the dimensions are
ordered as (x, y, z).
It is required that `size(ux) == size(uy) == size(uz) == size(u)`.
By default, `FDM` is set to the 3-point stencil of the first derivative.
`ax`, `ay` and `az` are the appropriate discretization factors
(1/dx^n, 1/dy^n, 1/dx^n for the n-th derivative);
if a single value `a` is given, it is expanded so that
`ax = ay = az = a`.
"""
@views function finitediff!(ux::A, u::A, a::Real, FDM=CFDM_3_1) where {A<:AbstractVector{Float64}}
n = length(u)
i_start = 1 + abs(FDM.grid[1])
i_end = n - FDM.grid[end]
for i in i_start:i_end
ux[i] = a * ∂x(u,i,FDM)
end # for
end # function
@views function finitediff!(
ux::A, uy::A, u::A,
ax::Real, ay::Real,
FDM=CFDM_3_1
) where {A<:AbstractMatrix{Float64}}
nx, ny = size(u)
i_start = j_start = 1 + abs(FDM.grid[1])
i_end = nx - FDM.grid[end]
j_end = ny - FDM.grid[end]
for j in j_start:j_end, i in i_start:i_end
ux[i,j] = ax * ∂x(u,i,j,FDM)
uy[i,j] = ay * ∂y(u,i,j,FDM)
end # for
end # function
finitediff!(ux::A, uy::A, u::A, a::Real, FDM=CFDM_3_1) where
{A<:AbstractMatrix{Float64}} = finitediff!(ux, uy, u, a, a, FDM)
@views function finitediff!(
ux::A, uy::A, uz::A, u::A,
ax::Real, ay::Real, az::Real,
FDM=CFDM_3_1
) where {A<:AbstractArray{Float64,3}}
nx, ny, nz = size(u)
i_start = j_start = k_start = 1 + abs(FDM.grid[1])
i_end = nx - FDM.grid[end]
j_end = ny - FDM.grid[end]
k_end = nz - FDM.grid[end]
for k in k_start:k_end, j in j_start:j_end, i in i_start:i_end
ux[i,j,k] = ax * ∂x(u,i,j,k,FDM)
uy[i,j,k] = ay * ∂y(u,i,j,k,FDM)
uz[i,j,k] = az * ∂z(u,i,j,k,FDM)
end # for
end # function
finitediff!(ux::A, uy::A, uz::A, u::A, a::Real, FDM=CFDM_3_1) where
{A<:AbstractArray{Float64,3}} = finitediff!(ux, uy, uz, u, a, a, a, FDM)
"""
laplacian!(du, u, a, FDM=CFDM_3_2)
laplacian!(du, u, ax, ay, FDM=CFDM_3_2)
laplacian!(du, u, ax, ay, az, FDM=CFDM_3_2)
Evaluate the finite-difference laplacian of `u` (∇²u),
storing the result in `du`.
By default, the 3-point stencil of the 2nd derivative is used.
"""
@views function laplacian!(du::A, u::A, a::Real, FDM=CFDM_3_2) where {A<:AbstractVector{Float64}}
finitediff!(du, u, a, FDM)
end # function
@views function laplacian!(
du::A, u::A,
ax::Real, ay::Real,
FDM=CFDM_3_2
) where {A<:AbstractMatrix{Float64}}
nx, ny = size(u)
i_start = j_start = 1 + abs(FDM.grid[1])
i_end = nx - FDM.grid[end]
j_end = ny - FDM.grid[end]
for j in j_start:j_end, i in i_start:i_end
du[i,j] = ax*∂x(u,i,j,FDM) + ay*∂y(u,i,j,FDM)
end # for
end # function
@views function laplacian!(
du::A, u::A,
ax::Real, ay::Real, az::Real,
FDM=CFDM_3_2
) where {A<:AbstractArray{Float64,3}}
nx, ny, nz = size(u)
i_start = j_start = k_start = 1 + abs(FDM.grid[1])
i_end = nx - FDM.grid[end]
j_end = ny - FDM.grid[end]
k_end = nz - FDM.grid[end]
for k in k_start:k_end, j in j_start:j_end, i in i_start:i_end
du[i,j,k] = ax*∂x(u,i,j,k,FDM) + ay*∂y(u,i,j,k,FDM) + az*∂z(u,i,j,k,FDM)
end # for
end
laplacian!(du, u, a::Real, FDM=CFDM_3_2) =
laplacian!(du, u, ntuple(_->a, ndims(u))..., FDM)
"""
divergence!(du, u, a, FDM=CFDM_3_1)
divergence!(du, ux, uy, ax, ay, FDM=CFDM_3_1)
divergence!(du, ux, uy, uz, ax, ay, az, FDM=CFDM_3_1)
Evaluate the finite-difference divergence of `u` (∇⋅u),
storing the result in `du`.
By default, the 3-point stencil of the 1st derivative is used.
"""
divergence!(du::A, u::A, a::Real, FDM=CFDM_3_1) where
{A<:AbstractVector{Float64}} = laplacian!(du, u, a, FDM)
@views function divergence!(
du::A, ux::A, uy::A,
ax::Real, ay::Real, FDM=CFDM_3_1
) where {A<:AbstractMatrix{Float64}}
nx, ny = size(du)
i_start = j_start = 1 + abs(FDM.grid[1])
i_end = nx - FDM.grid[end]
j_end = ny - FDM.grid[end]
for j in j_start:j_end, i in i_start:i_end
du[i,j] = ax*∂x(ux,i,j,FDM) + ay*∂y(uy,i,j,FDM)
end # for
end # function
@views function divergence!(
du::A, ux::A, uy::A, uz::A,
ax::Real, ay::Real, az::Real,
FDM=CFDM_3_1
) where {A<:AbstractArray{Float64,3}}
nx, ny, nz = size(du)
i_start = j_start = k_start = 1 + abs(FDM.grid[1])
i_end = nx - FDM.grid[end]
j_end = ny - FDM.grid[end]
k_end = nz - FDM.grid[end]
for k in k_start:k_end, j in j_start:j_end, i in i_start:i_end
du[i,j,k] = ax*∂x(ux,i,j,k,FDM) + ay*∂y(uy,i,j,k,FDM) + az*∂z(uz,i,j,k,FDM)
end # for
end
| Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 1793 | export AbstractMicrobe, Microbe
"""
AbstractMicrobe{D} <: AbstractAgent where {D<:Integer}
YourMicrobeType{D} <: AbstractMicrobe{D}
All microbe types in Bactos.jl simulations must be instances
of user-defined types that are subtypes of `AbstractMicrobe`.
The parameter `D` defines the dimensionality of the space in which the
microbe type lives (1, 2 and 3 are currently supported).
All microbe types should have the following fields:
`- id::Int` → id of the microbe
`- pos::NTuple{D,Float64}` → position of the microbe
`- vel::NTuple{D,Float64}` → velocity of the microbe
`- motility` → motile pattern of the microbe
`- turn_rate::Float64` → average reorientation rate of the microbe
`- rotational_diffusivity::Float64` → rotational diffusion coefficient
"""
abstract type AbstractMicrobe{D} <: AbstractAgent where {D<:Integer} end
"""
Microbe{D} <: AbstractMicrobe{D}
Basic microbe type for simple simulations.
Default parameters:
- `id::Int` → identifier used internally by Agents.jl
- `pos::NTuple{D,Float64} = ntuple(zero,D)` → position
- `motility = RunTumble()` → motile pattern
- `vel::NTuple{D,Float64} = rand_vel(D) .* rand(motility.speed)` → velocity vector
- `turn_rate::Float64 = 1.0` → frequency of reorientations
- `state::Float64` → generic variable for a scalar internal state
- `rotational_diffusivity::Float64 = 0.0` → rotational diffusion coefficient
- `radius::Float64 = 0.0` → equivalent spherical radius of the microbe
"""
Base.@kwdef mutable struct Microbe{D} <: AbstractMicrobe{D}
id::Int
pos::NTuple{D,Float64} = ntuple(zero, D)
motility = RunTumble()
vel::NTuple{D,Float64} = rand_vel(D, motility)
turn_rate::Float64 = 1.0
state::Float64 = 0.0
rotational_diffusivity::Float64 = 0.0
radius::Float64 = 0.0
end # struct | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 3066 | export
initialise_model, initialise_ode, initialise_pathfinder
"""
initialise_model(;
microbes,
timestep,
extent, spacing = extent/20, periodic = true,
random_positions = true,
model_properties = Dict(),
)
Initialise an `AgentBasedModel` from population `microbes`.
Requires the integration `timestep` and the `extent` of the simulation box.
When `random_positions = true` the positions assigned to `microbes` are
ignored and new ones, extracted randomly in the simulation box, are assigned;
if `random_positions = false` the original positions in `microbes` are kept.
Any extra property can be assigned to the model via the `model_properties`
dictionary.
"""
function initialise_model(;
microbes,
timestep,
extent, spacing = minimum(extent)/20, periodic = true,
random_positions = true,
model_properties = Dict(),
)
space_dim = length(microbes[1].pos)
if typeof(extent) <: Real
domain = Tuple(fill(extent, space_dim))
else
if length(extent) ≠ space_dim
error("Space extent and microbes must have the same dimensionality.")
end # if
domain = extent
end # if
properties = Dict(
:t => 0,
:timestep => timestep,
:compound_diffusivity => 608.0,
:concentration_field => (pos,model) -> 0.0,
:concentration_gradient => (pos,model) -> zero.(pos),
:concentration_time_derivative => (pos,model) -> 0.0,
model_properties...
)
space = ContinuousSpace(
domain,
spacing = spacing,
periodic = periodic
)
# falls back to eltype(microbes) if there is a single microbe type,
# builds a Union type if eltype(microbes) is abstract
MicrobeType = Union{typeof.(microbes)...}
model = ABM(
MicrobeType, space;
properties,
scheduler = Schedulers.fastest,
)
for microbe in microbes
if random_positions
add_agent!(microbe, model)
else
add_agent!(microbe, microbe.pos, model)
end # if
end # for
return model
end # function
"""
initialise_ode(ode_step!, u₀, p; alg=Tsit5(), kwargs...)
Initialise an OrdinaryDiffEq integrator, using the in-place stepping algorithm
`ode_step!`, initial conditions `u₀` and parameters `p`.
Default integration algorithm is `Tsit5` (others can be accessed by importing
OrdinaryDiffEq).
Any extra parameter can be passed over to the integrator via kwargs.
"""
function initialise_ode(ode_step!, u₀, p; alg=Tsit5(), kwargs...)
prob = ODEProblem(ode_step!, u₀, (0.0, Inf), p)
integrator = init(prob, alg; kwargs...)
return integrator
end # function
function initialise_pathfinder(
extent::Real, periodic::Bool,
walkmap::BitArray{D}
) where D
initialise_pathfinder(ntuple(_->extent,D), periodic, walkmap)
end
function initialise_pathfinder(
extent::NTuple{D,<:Real}, periodic::Bool,
walkmap::BitArray{D}
) where D
space = ContinuousSpace(extent; periodic)
AStar(space; walkmap)
end | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 4103 | export
AbstractMotility, AbstractMotilityOneStep, AbstractMotilityTwoStep,
MotileState, TwoState, Forward, Backward, switch!,
RunTumble, RunReverse, RunReverseFlick
"""
AbstractMotility
General abstract interface for motility patterns.
"""
abstract type AbstractMotility end
"""
AbstractMotilityOneStep
One-step motility patterns (`RunTumble`).
Subtypes must have at least the following fields:
- `speed`: distribution of microbe speed, new values extracted after each turn
- `polar`: distribution of polar angles
- `azimuthal`: distribution azimuthal angles
For 2-dimensional microbe types, only `polar` defines reorientations and `azimuthal` is ignored.
"""
abstract type AbstractMotilityOneStep <: AbstractMotility end
"""
AbstractMotilityTwoStep
Two-step motility patterns (`RunReverse` and `RunReverseFlick`), with different
properties between forward and backward state of motion.
Subtypes must have at least the following fields:
- `speed_forward`: distribution of microbe speed, new values extracted after each turn
- `polar_forward`: distribution of in-plane reorientations for motile state 0
- `azimuthal_forward`: distribution of out-of-plane reorientations for motile state 0
- `speed_backward`: distribution of microbe speed, new values extracted after each turn
- `polar_backward`: distribution of in-plane reorientations for motile state 1
- `azimuthal_backward`: distribution of out-of-plane reorientations for motile state 1
- `motile_state`: defines current motile state (e.g. `Forward` or `Backward` for a `TwoState`)
For 2-dimensional microbe types, only `polar_forward` and `polar_backward` define reorientations,
while `azimuthal_forward` and `azimuthal_forward` are ignored.
"""
abstract type AbstractMotilityTwoStep <: AbstractMotility end
# just a wrapper to allow state to be mutable
mutable struct MotileState
state
end
MotileState() = MotileState(TwoState())
"""
TwoState <: Enum{Bool}
Represents the state of a two-step motile pattern, can take values
`Forward` or `Backward`.
"""
@enum TwoState::Bool Forward Backward
Base.show(io::IO, ::MIME"text/plain", x::TwoState) =
x == Forward ? print(io, "Forward") : print(io, "Backward")
# choose at random between Forward and Backward if not specified
"""
TwoState([rng::AbstractRng])
Randomly generate the state of a two-step motile pattern.
"""
TwoState() = TwoState(Random.default_rng())
TwoState(rng::AbstractRNG) = TwoState(rand(rng, (true, false)))
# overload getproperty and setproperty! for more convenient access to state
function Base.getproperty(obj::AbstractMotilityTwoStep, sym::Symbol)
if sym === :state
return obj.motile_state.state
else
return getfield(obj, sym)
end
end
function Base.setproperty!(value::AbstractMotilityTwoStep, name::Symbol, x)
if name === :state
return setfield!(value.motile_state, :state, x)
else
return setfield!(obj, name, x)
end
end
# define rules for switching motile state
switch!(::AbstractMotilityOneStep) = nothing
"""
switch!(m::AbstractMotilityTwoStep)
Switch the state of a two-step motility pattern (`m.state`)
from `Forward` to `Backward` and viceversa.
"""
switch!(m::AbstractMotilityTwoStep) = (m.state = ~m.state; nothing)
Base.:~(x::TwoState) = TwoState(~Bool(x))
Base.@kwdef struct RunTumble <: AbstractMotilityOneStep
speed = Degenerate(30.0)
polar = Uniform(-π, π)
azimuthal = Arccos(-1, 1)
end # struct
Base.@kwdef struct RunReverse <: AbstractMotilityTwoStep
speed_forward = Degenerate(30.0)
polar_forward = Degenerate(π)
azimuthal_forward = Arccos(-1,1)
speed_backward = speed_forward
polar_backward = polar_forward
azimuthal_backward = azimuthal_forward
motile_state = MotileState()
end # struct
Base.@kwdef struct RunReverseFlick <: AbstractMotilityTwoStep
speed_forward = Degenerate(30.0)
polar_forward = Degenerate(π)
azimuthal_forward = Arccos(-1,1)
speed_backward = speed_forward
polar_backward = [-π/2, π/2]
azimuthal_backward = Arccos(-1,1)
motile_state = MotileState()
end # struct | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 2752 | export msd
"""
unfold_coord(x₀, x₁, L)
Unfold a translation `x₀` ↦ `x₁` in a domain of periodicity `L`.
"""
function unfold_coord(x₀, x₁, L)
dx = x₁ - x₀
sdx = sign(dx)
a = round(abs(dx/L))
if abs(dx) > L/2
return x₁ - a*L*sdx
else
return x₁
end # if
end # function
"""
unfold!(unfolded, cnf₁, cnf₀, L)
Unfold spatial configuration `cnf₁` with respect to `cnf₀` in a domain of
periodicity `L` and store to `unfolded`.
"""
function unfold!(unfolded, cnf₁, cnf₀, L)
dim = length(first(cnf₁))
nmicrobes, = size(cnf₁)
for i in 1:nmicrobes
l = typeof(L) <: AbstractArray ? L[μ] : L
newx = ntuple(μ -> unfold_coord(cnf₀[i][μ], cnf₁[i][μ], l), dim)
unfolded[i] = newx
end # for
end # function
"""
unfold(trajectory::T, L) where {S<:Tuple, T<:AbstractArray{S,2}}
Unfold `trajectory` in a domain of periodicity `L`.
"""
function unfold(trajectory::T, L) where {S<:Tuple, T<:AbstractArray{S,2}}
nmicrobes, nsteps = size(trajectory)
unfolded = Matrix{eltype(trajectory)}(undef, size(trajectory)...)
unfolded[:,1] .= trajectory[:,1]
for t in 2:nsteps
oldcnf = unfolded[:,t-1]
newcnf = trajectory[:,t]
unfolded_slice = @view unfolded[:,t]
unfold!(unfolded_slice, newcnf, oldcnf, L)
end # for
return unfolded
end # function
"""
msd(adf; tstep::Int=1, L=Inf)
Evaluate mean-squared displacement from an agent dataframe `adf` containing
the position timeseries of agents (`:pos` field).
Assumes that sampled positions are uniformly spaced in time.
Parameter `L` defines the periodicity of the domain for unfolding;
set `L=Inf` (default) if boundaries are not periodic.
msd(trajectory::T, tstep::Int=1) where {S,T<:AbstractArray{S,2}}
Evaluate mean-squared displacement of `trajectory`, where different microbes
are collected along first dimension, and times along second dimension.
"""
function msd(adf; tstep::Int=1, L=Inf)
trajectory = vectorize_adf_measurement(adf, :pos)
if isinf(L)
return msd(trajectory, tstep)
else
trajectory_unfolded = unfold(trajectory, L)
return msd(trajectory_unfolded, tstep)
end # if
end # function
function msd(trajectory::T, tstep::Int=1) where {S,T<:AbstractArray{S,2}}
nmicrobes, nsteps = size(trajectory)
timelags = range(1, nsteps-1; step=tstep)
MSD = zeros(nsteps-1)
for (j,Δt) in enumerate(timelags)
for t₀ in 1:nsteps-Δt
for i in 1:nmicrobes
u = trajectory[i, t₀]
v = trajectory[i, t₀+Δt]
MSD[j] += sum(abs2.(u .- v))
end # for
end # for
MSD[j] /= (nmicrobes * (nsteps-j))
end # for
return MSD
end # function | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 3999 | export ObstacleSphere, get_walkmap, stick!, glide!, bounce!
"""
struct ObstacleSphere{D}
pos::NTuple{D,Float64}
radius::Float64
affect!::Function
end
Spherical obstacle in a D-dimensional space.
- `pos`: center position of the sphere
- `radius`: radius of the sphere
- `affect!`: function with signature `(microbe,sphere,model)`, defines microbe-sphere interaction.
Three `affect!` functions are provided out-of-the box:
`stick!`, `glide!` and `bounce!`.
"""
struct ObstacleSphere{D}
pos::NTuple{D,Float64}
radius::Float64
affect!::Function
end # struct
ObstacleSphere(pos::NTuple{D,<:Real}, radius::Real,
affect!::Function = (_,_,_) -> nothing
) where D = ObstacleSphere{D}(Float64.(pos), Float64(radius), affect!)
function initialise_pathfinder(
extent, periodic::Bool,
r::Real, spheres::AbstractVector{ObstacleSphere{D}};
Δ::Real=r/2
) where D
walkmap = get_walkmap(extent, r, spheres; Δ)
initialise_pathfinder(extent, periodic, walkmap)
end
function get_walkmap(
extent::NTuple{D,<:Real}, r::Real,
spheres::AbstractVector{ObstacleSphere{D}};
Δ::Real=r/2
)::BitArray{D} where D
mesh = ntuple(i -> 0:Δ:extent[i], D)
itr = Iterators.product(mesh...)
return BitArray([is_walkable(pos, r, spheres) for pos in itr])
end
function is_walkable(
pos::NTuple{D,<:Real}, r::Real,
spheres::AbstractVector{ObstacleSphere{D}}
)::Bool where D
for sphere in spheres
if !is_walkable(pos, r, sphere)
return false
end
end
return true
end
function is_walkable(
pos::NTuple{D,<:Real}, r::Real,
sphere::ObstacleSphere{D}
)::Bool where D
norm(pos .- sphere.pos) ≥ r + sphere.radius
end
"""
stick!(microbe, sphere::ObstacleSphere, model)
`microbe` sticks to the `sphere` surface at the point of contact.
The orientation of the microbe is unchanged.
"""
function stick!(microbe, sphere::ObstacleSphere, model)
x = microbe.pos
y = sphere.pos
R = microbe.radius + sphere.radius
d = norm(x .- y)
if d < R
s = @. -microbe.vel * model.timestep
a = sum(abs2.(s))
b = 2.0 * dot(x.-y, s)
c = d*d - R*R
ε = -b/2a * (1 - sqrt(1 - 4*a*c/(b*b)))
z = @. ε*s
walk!(microbe, z, model)
end # if
end # function
"""
glide!(microbe, sphere::ObstacleSphere, model)
`microbe` sticks to the `sphere` surface while gliding along.
"""
function glide!(microbe, sphere::ObstacleSphere, model)
x = microbe.pos
y = sphere.pos
R = microbe.radius + sphere.radius
d = norm(x .- y)
if d < R
s = y .- x
a = sum(abs2.(s))
c = d*d - R*R
ε = 1 - sqrt(1 - c/a)
z = @. ε*s
walk!(microbe, z, model)
end # if
end # function
"""
bounce!(microbe, sphere::ObstacleSphere, model; ζ=1.0)
`microbe` is reflected off the `sphere` surface, inverting
the direction of its `vel` field.
The parameter `ζ` is the elastic coefficient of the collision;
for `ζ=1` the collision is perfectly elastic (microbe run length is conserved);
for `ζ=0` the microbe sticks to the surface (but vel is inverted).
"""
function bounce!(microbe, sphere::ObstacleSphere, model; ζ=1.0)
if !(0 ≤ ζ ≤ 1)
throw(DomainError(ζ, "ζ must have value in the range [0,1]."))
end # if
x = microbe.pos
y = sphere.pos
R = microbe.radius + sphere.radius
d = norm(x .- y)
if d < R
s = @. -microbe.vel * model.timestep
a = sum(abs2.(s))
b = 2.0 * dot(x.-y, s)
c = d*d - R*R
ε = -b/2a * (1 - sqrt(1 - 4*a*c/(b*b)))
z = @. (1+ζ)*ε*s
# hit surface
z₁ = @. ε*s
walk!(microbe, z₁, model)
# reorient
r_hat = (y.-x)./d
deflection = -2 .* dot(microbe.vel, r_hat) .* r_hat
microbe.vel = @. ζ * (microbe.vel + deflection)
# bounce
z₂ = @. ε * (microbe.vel * model.timestep)
walk!(microbe, z₂, model)
end # if
end # function | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 2437 | export
rotate, turn!, rotational_diffusion!
rotate(w::SVector{1}) = -w
rotate(w::SVector{1}, θ) = rotate(w)
rotate(w::SVector{1}, θ, ϕ) = rotate(w)
rotate(w::SVector{2}, θ) = Angle2d(θ) * w
rotate(w::SVector{2}, θ, ϕ) = rotate(w, θ)
function rotate(w::SVector{3}, θ, ϕ)
m = findfirst(w .≠ 0)
n = m%3 + 1
u = SVector(0., 0., 0.)
u = setindex(u, w[m], n)
u = setindex(u, -w[n], m)
# rotate w around its normal u
a = AngleAxis(θ, u...) * w
# rotate a around the original w direction
return AngleAxis(ϕ, w...) * a
end # function
rotate(w::Tuple, θ, ϕ) = rotate(SVector(w), θ, ϕ)
rotate(w::Tuple, θ) = rotate(SVector(w), θ)
function turn!(microbe::AbstractMicrobe, motility::AbstractMotilityOneStep)
# store actual speed
U₀ = norm(microbe.vel)
# perform reorientation
θ = rand(motility.polar)
ϕ = rand(motility.azimuthal)
microbe.vel = rotate(microbe.vel, θ, ϕ) |> Tuple
# extract new speed from distribution
U₁ = rand(motility.speed)
# update speed
microbe.vel = microbe.vel .* (U₁ / U₀)
return nothing
end # function
function turn!(microbe::AbstractMicrobe, motility::AbstractMotilityTwoStep)
# store current speed
U₀ = norm(microbe.vel)
# perform reorientation depending on current motile state
if motility.state == Forward
# reorient according to forward-state angles
θ = rand(motility.polar_forward)
ϕ = rand(motility.azimuthal_forward)
# extract new speed from backward-state distribution
U₁ = rand(motility.speed_backward)
elseif motility.state == Backward
# reorient according to backward-state angles
θ = rand(motility.polar_backward)
ϕ = rand(motility.azimuthal_backward)
# extract new speed from forward-state distribution
U₁ = rand(motility.speed_forward)
end # if
# reorient
microbe.vel = rotate(microbe.vel, θ, ϕ) |> Tuple
# switch motile state
switch!(motility)
# update speed
microbe.vel = microbe.vel .* (U₁ / U₀)
return nothing
end # function
rotational_diffusion!(microbe::AbstractMicrobe{1}, dt) = nothing
function rotational_diffusion!(microbe::AbstractMicrobe, dt)
D_rot = microbe.rotational_diffusivity
σ = sqrt(2*D_rot*dt)
polar = rand(Normal(0, σ))
azimuthal = rand(Arccos())
microbe.vel = Tuple(rotate(microbe.vel, polar, azimuthal))
return nothing
end # function | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 1043 | export
microbe_step!
function microbe_step!(
microbe::AbstractMicrobe, model::ABM;
affect! = (microbe, model) -> nothing,
turnrate = (microbe, model) -> microbe.turn_rate,
)
dt = model.timestep # integration timestep
# update microbe position
if haskey(model.properties, :pathfinder)
pathfinder_step!(microbe, model, dt)
else
move_agent!(microbe, model, dt)
end
# reorient microbe due to rotational diffusion
rotational_diffusion!(microbe, dt)
# update microbe state
affect!(microbe, model)
# update reorientation rate
ω = turnrate(microbe, model)
if rand() < ω*dt # if true reorient microbe
turn!(microbe, microbe.motility)
end # if
return nothing
end # function
function pathfinder_step!(microbe::AbstractMicrobe, model::ABM, dt::Real)
target_position = microbe.pos .+ microbe.vel .* dt
U = norm(microbe.vel)
plan_route!(microbe, target_position, model.pathfinder)
move_along_route!(microbe, model, model.pathfinder, U, dt)
end | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 687 | export model_step!
"""
model_step!(model; update_model! = (model) -> nothing)
Update model properties through the `update_model!` function
(defaults to nothing).
If `model` contains an OrdinaryDiffEq integrator among its
properties (`model.integrator`), also perform an integration step.
"""
function model_step!(model;
update_model!::Function = (model) -> nothing
)
# if a diffeq integrator is provided, integrate over a timestep
if haskey(model.properties, :integrator)
step!(model.integrator, model.timestep, true)
end # if
# increase step count
model.t += 1
# update model properties
update_model!(model)
return nothing
end # function | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 1734 | export
rand_vel, rand_speed, vectorize_adf_measurement
"""
rand_vel([rng,] N)
Generate a random N-tuple of unitary norm.
"""
function rand_vel(D::Int)
v = rand(D) .* 2 .- 1
Tuple(v ./ norm(v))
end # function
function rand_vel(rng, D::Int)
v = rand(rng, D) .* 2 .- 1
Tuple(v ./ norm(v))
end # function
"""
rand_speed(m::AbstractMotilityOneStep)
Extract value from the speed distribution of the motility pattern `m.speed`.
"""
rand_speed(m::AbstractMotilityOneStep) = rand(m.speed)
"""
rand_speed(m::AbstractMotilityTwoStep)
Extract value from the speed distribution of the motility pattern.
If `motilestate(m) == ForwardState()` extract from `speed_forward`, otherwise
from `speed_backward`.
"""
function rand_speed(m::AbstractMotilityTwoStep)
if m.state == Forward
return rand(m.speed_forward)
else
return rand(m.speed_backward)
end
end
"""
rand_vel([rng,] N::Int, m::AbstractMotility)
Generate a random N-tuple, with norm defined by the speed distribution of `m`.
"""
rand_vel(D::Int, m::AbstractMotility) = rand_vel(D) .* rand_speed(m)
rand_vel(rng, D::Int, m::AbstractMotility) = rand_vel(rng, D) .* rand_speed(m)
"""
vectorize_adf_measurement(adf, sym)
Collect quantity `sym` from the agent dataframe `adf` and return it in matrix
form with dimensions (microbes, times).
"""
function vectorize_adf_measurement(adf, sym)
nmicrobes = unique(adf[!,:id]) |> length
nsteps = unique(adf[!,:step]) |> length
datatype = typeof(adf[1,sym])
s = Matrix{datatype}(undef, nmicrobes, nsteps)
for t in 1:nsteps
for i in 1:nmicrobes
s[i,t] = adf[i + (t-1)*nmicrobes, sym]
end # for
end # for
return s
end # function
| Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 3578 | export AbstractXie, Xie, XieNoisy, xie_affect!, xie_turnrate
abstract type AbstractXie{D} <: AbstractMicrobe{D} end
Base.@kwdef mutable struct Xie{D} <: AbstractXie{D}
id::Int
pos::NTuple{D,Float64} = ntuple(zero, D)
motility = RunReverseFlick(speed_forward = Degenerate(46.5))
vel::NTuple{D,Float64} = rand_vel(D, motility)
turn_rate_forward::Float64 = 2.3 # 1/s
turn_rate_backward::Float64 = 1.9 # 1/s
state_m::Float64 = 0.0 # s
state_z::Float64 = 0.0 # s
state::Float64 = 0.0 # s
adaptation_time_m::Float64 = 1.29 # s
adaptation_time_z::Float64 = 0.28 # s
gain_forward::Float64 = 2.7 # 1/s
gain_backward::Float64 = 1.6 # 1/s
binding_affinity::Float64 = 0.39 # μM
rotational_diffusivity::Float64 = 0.26 # rad²/s
radius::Float64 = 0.5 # μm
end
Base.@kwdef mutable struct XieNoisy{D} <: AbstractXie{D}
id::Int
pos::NTuple{D,Float64} = ntuple(zero, D)
motility = RunReverseFlick(speed_forward = Degenerate(46.5))
vel::NTuple{D,Float64} = rand_vel(D, motility)
turn_rate_forward::Float64 = 2.3 # 1/s
turn_rate_backward::Float64 = 1.9 # 1/s
state_m::Float64 = 0.0 # s
state_z::Float64 = 0.0 # s
state::Float64 = 0.0 # s
adaptation_time_m::Float64 = 1.29 # s
adaptation_time_z::Float64 = 0.28 # s
gain_forward::Float64 = 2.7 # 1/s
gain_backward::Float64 = 1.6 # 1/s
binding_affinity::Float64 = 0.39 # μM
chemotactic_precision::Float64 = 6.0 # 1
rotational_diffusivity::Float64 = 0.26 # rad²/s
radius::Float64 = 0.5 # μm
end
function xie_affect!(microbe::Xie, model)
Δt = model.timestep
c = model.concentration_field(microbe.pos, model)
K = microbe.binding_affinity
ϕ = log(1.0 + c/K)
τ_m = microbe.adaptation_time_m
τ_z = microbe.adaptation_time_z
a₀ = (τ_m*τ_z)/(τ_m - τ_z)
m = microbe.state_m
z = microbe.state_z
m += (ϕ - m/τ_m)*Δt
z += (ϕ - z/τ_z)*Δt
microbe.state_m = m
microbe.state_z = z
microbe.state = a₀ * (m/τ_m - z/τ_z)
return nothing
end
function xie_affect!(microbe::XieNoisy, model; ε=1e-16)
Δt = model.timestep
Dc = model.compound_diffusivity
c = model.concentration_field(microbe.pos, model)
K = microbe.binding_affinity
a = microbe.radius
Π = microbe.chemotactic_precision
σ = Π * 0.04075 * sqrt(3*c / (5*π*Dc*a*Δt))
M = rand(Normal(c,σ))
ϕ = log(1.0 + max(M/K, -1+ε))
τ_m = microbe.adaptation_time_m
τ_z = microbe.adaptation_time_z
a₀ = (τ_m*τ_z)/(τ_m - τ_z)
m = microbe.state_m
z = microbe.state_z
m += (ϕ - m/τ_m)*Δt
z += (ϕ - z/τ_z)*Δt
microbe.state_m = m
microbe.state_z = z
microbe.state = a₀ * (m/τ_m - z/τ_z)
return nothing
end
function xie_turnrate(microbe, model)
if microbe.motility isa AbstractMotilityTwoStep
return xie_turnrate_twostep(microbe, model)
else
return xie_turnrate_onestep(microbe, model)
end
end
function xie_turnrate_onestep(microbe, model)
S = microbe.state
ν₀ = microbe.turn_rate_forward
β = microbe.gain_forward
return ν₀*(1 + β*S)
end
function xie_turnrate_twostep(microbe, model)
S = microbe.state
if microbe.motility.state == Forward
ν₀ = microbe.turn_rate_forward
β = microbe.gain_forward
else
ν₀ = microbe.turn_rate_backward
β = microbe.gain_backward
end
return ν₀*(1 + β*S)
end
function microbe_step!(microbe::AbstractXie, model::ABM)
microbe_step!(
microbe, model;
affect! = xie_affect!,
turnrate = xie_turnrate
)
end | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 4005 | using Test, Bactos, Random
@testset "Finite differences" begin
≃(x,y) = isapprox(x,y;atol=1e-3) # \simeq
@testset "One dimension" begin
n = 256
x = range(0, 2π; length=n)
# reset x with ghost cells
m = 2
dx = x.step.hi
x = range(x[1]-m*dx, x[end]+m*dx; step=dx)
# initial function
y₀ = sin.(x)
# analytical first derivative
y₁ = cos.(x)
# analytical second derivative
y₂ = -sin.(x)
# initialize arrays for numerical derivatives
dy₀ = zero(y₀)
d²y₀ = zero(y₀)
ddy₀ = zero(y₀)
dy₁ = zero(y₀)
∇y₀ = zero(y₀)
∇²y₀ = zero(y₀)
divy₀ = zero(y₀)
# evaluate numerical derivatives
# first derivative
finitediff!(dy₀, y₀, 1/dx)
# first derivative of analytical first derivative
finitediff!(dy₁, y₁, 1/dx)
# first derivative of numerical first derivative
finitediff!(ddy₀, dy₀, 1/dx)
# second derivative
finitediff!(d²y₀, y₀, 1/dx^2, CFDM_3_2)
# with a 1st order stencil, laplacian equates first derivative
laplacian!(∇y₀, y₀, 1/dx, CFDM_3_1)
# actual laplacian, in 1d corresponds to second derivative
laplacian!(∇²y₀, y₀, 1/dx^2)
# divergence, in 1d corresponds to first derivative
divergence!(divy₀, y₀, 1/dx)
# ghost cells must be excluded from the test
@test all((dy₀ .≃ y₁)[1+m:end-m])
@test all((dy₁ .≃ y₂)[1+m:end-m])
@test all((ddy₀ .≃ y₂)[1+m:end-m])
@test all((d²y₀ .≃ y₂)[1+m:end-m])
@test ∇y₀ == dy₀
@test ∇²y₀ == d²y₀
@test divy₀ == dy₀
end
@testset "Two dimensions" begin
nx = 256
ny = 512
x = range(0, 2π; length=nx)
y = range(0, 2π; length=ny)
# reset x and y with ghost cells
m = 2
dx = x.step.hi
dy = y.step.hi
x = range(x[1]-m*dx, x[end]+m*dx; step=dx)
y = range(y[1]-m*dy, y[end]-m*dy; step=dy)
u₀ = @. sin(x) * cos(y)'
ux = @. cos(x) * cos(y)'
uy = @. - sin(x) * sin(y)'
lapu = @. -2 * u₀
myux = zero(u₀)
myuy = zero(u₀)
mylapu = zero(u₀)
mylapu_2 = zero(u₀)
finitediff!(myux, myuy, u₀, 1/dx, 1/dy)
laplacian!(mylapu, u₀, 1/dx^2, 1/dy^2)
divergence!(mylapu_2, myux, myuy, 1/dx, 1/dy)
@test all((myux .≃ ux)[1+m:end-m,1+m:end-m])
@test all((myuy .≃ uy)[1+m:end-m,1+m:end-m])
@test all((mylapu .≃ lapu)[1+m:end-m,1+m:end-m])
@test all((mylapu_2 .≃ lapu)[1+m:end-m,1+m:end-m]) # ∇⋅∇ = ∇²
end
@testset "Three dimensions" begin
nx = 128
ny = 128
nz = 64
x₁, x₂ = 0.0, 2π
y₁, y₂ = 0.0, 2π
z₁, z₂ = 0.0, 1.0
dx = (x₂-x₁)/(nx-1)
dy = (y₂-y₁)/(ny-1)
dz = (z₂-z₁)/(nz-1)
# domain with ghost cells
m = 2
x = range(x₁-m*dx, x₂+m*dx; step=dx)
y = range(y₁-m*dy, y₂+m*dy; step=dy)
z = range(z₁-m*dz, z₂+m*dz; step=dz)
u₀ = zeros(nx+2m, ny+2m, nz+2m)
ux = zero(u₀)
uy = zero(u₀)
uz = zero(u₀)
∇²u = zero(u₀)
for k in axes(u₀,3), j in axes(u₀,2), i in axes(u₀,1)
u₀[i,j,k] = cos(x[i])*sin(y[j])*z[k]
ux[i,j,k] = -sin(x[i])*sin(y[j])*z[k]
uy[i,j,k] = cos(x[i])*cos(y[j])*z[k]
uz[i,j,k] = cos(x[i])*sin(y[j])
∇²u[i,j,k] = -2*u₀[i,j,k]
end
myux = zero(u₀)
myuy = zero(u₀)
myuz = zero(u₀)
my∇²u = zero(u₀)
finitediff!(myux, myuy, myuz, u₀, 1/dx, 1/dy, 1/dz)
laplacian!(my∇²u, u₀, 1/dx^2, 1/dy^2, 1/dz^2)
@test all((myux .≃ ux)[m+1:end-m,m+1:end-m,m+1:end-m])
@test all((myuy .≃ uy)[m+1:end-m,m+1:end-m,m+1:end-m])
@test all((myuz .≃ uz)[m+1:end-m,m+1:end-m,m+1:end-m])
@test all((my∇²u .≃ ∇²u)[m+1:end-m,m+1:end-m,m+1:end-m])
end
end | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 4088 | using Test, Bactos, Random
@testset "Measurements" begin
≃(x,y) = isapprox(x,y,atol=1e-8) # \simeq
@testset "Chemotactic drift velocity" begin
# with turn_rate=0 motility is ignored and vel never changes
m1 = Microbe{1}(id=1, pos=(4.0,), vel=(1.0,), turn_rate=0)
m2 = Microbe{1}(id=2, pos=(6.0,), vel=(-1.0,), turn_rate=0)
m3 = Microbe{1}(id=3, pos=(3.0,), vel=(3.0,), turn_rate=0)
dt = 1.0
L = 10.0
target_point = (5.0,)
target_direction = (1.0,)
model = initialise_model(;
microbes = [m1, m2, m3],
timestep = dt,
extent = L,
random_positions = false
)
adata = [:pos, :vel]
adf, = run!(model, microbe_step!, 2; adata)
adf1 = filter(:id => id -> id==1, adf; view=true)
adf2 = filter(:id => id -> id==2, adf; view=true)
adf3 = filter(:id => id -> id==3, adf; view=true)
vd1_dir = driftvelocity_direction(adf1, target_direction)
vd1_pnt = driftvelocity_point(adf1, target_point)
vd2_dir = driftvelocity_direction(adf2, target_direction)
vd2_pnt = driftvelocity_point(adf2, target_point)
vd3_pnt = driftvelocity_point(adf3, target_point)
vd3_pnt_n = driftvelocity_point(adf3, target_point; normalize=true)
# m1 is moving along target_direction at all timepoints
@test vd1_dir == [1.0 1.0 1.0]
# m1 is moving towards target_point at initial timepoint
@test vd1_pnt[1] == 1.0
# at final timepoint, m1 overshoots target_point and moves in opposite direction
@test vd1_pnt[3] == -1.0
# m2 is moving against target_direction at all timepoints
@test vd2_dir == [-1.0 -1.0 -1.0]
# m2 is moving towards target_point at initial timepoint
@test vd2_pnt[1] == 1.0
# at final timepoint, m2 overshoots target_point and moves in opposite direction
@test vd2_pnt[3] == -1.0
# same as m1, but now test if normalize kwarg works
# not normalized
@test vd3_pnt[1] == 3.0
@test vd3_pnt[3] == -3.0
# normalized
@test vd3_pnt_n[1] == 1.0
@test vd3_pnt_n[3] == -1.0
end
@testset "Mean-squared displacement" begin
U = 2.0
extent = 50.0
# if turn_rate=0 motility is ignored and vel never changes
# so the microbe is moving ballistically with speed U
microbes = [Microbe{1}(id=0, turn_rate=0, vel=(U,), pos=(extent/2,))]
timestep = 0.1
model = initialise_model(; microbes, extent, timestep,
random_positions=false)
adata = [:pos]
nsteps = 10
adf, = run!(model, microbe_step!, nsteps; adata)
# total displacement obeys ballistic motion
Δx = adf[end,:pos][1] .- adf[1,:pos][1]
@test Δx ≃ U*nsteps*timestep
MSD = msd(adf) |> vec
# for ballistic motion MSD(t) = U²t²
for n in 1:nsteps
@test MSD[n] ≃ (U*n*timestep)^2
end # for
# same ballistic test over longer times
# this time using `L=extent` keyword to unwrap periodic boundaries
nsteps = 500
adf, = run!(model, microbe_step!, nsteps; adata)
MSD = msd(adf; L=extent) |> vec
@test MSD[nsteps] ≃ (U*nsteps*timestep)^2
U = 3.0
# turn_rate=Inf in 1D means that the bacterium is reversing at each step
microbes = [Microbe{1}(id=0, turn_rate=Inf, vel=(U,),
motility=RunTumble(speed=Degenerate(U)))]
extent = 50.0
timestep = 0.1
model = initialise_model(; microbes, extent, timestep)
nsteps = 4
adf, = run!(model, microbe_step!, nsteps; adata)
MSD = msd(adf; L=extent) |> vec
# first step is ballistic forward
@test MSD[1] ≃ (U*timestep)^2
# second step goes back to initial position
@test MSD[2] ≃ 0.0
# same pattern for following timesteps
@test MSD[3] ≃ MSD[1]
@test MSD[4] ≃ MSD[2]
end
end | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 6291 | using Test, Bactos, Random
using LinearAlgebra: norm
@testset "Microbe creation" begin
@testset "Default microbe" begin
# test type hierarchy
@test Microbe <: AbstractMicrobe
@test Microbe{1} <: AbstractMicrobe
@test Microbe{2} <: AbstractMicrobe
@test Microbe{3} <: AbstractMicrobe
# test errors for missing arguments
@test_throws UndefKeywordError Microbe{3}()
@test_throws UndefVarError Microbe(id=0)
# test arguments behave as expected, 2D
id = rand(Int)
m = Microbe{2}(id=id)
@test m.id == id
@test m.pos isa NTuple{2,Float64}
@test all(m.pos .== 0.0)
@test norm(m.vel) ≈ 30.0
@test typeof(m.motility) == RunTumble
@test m.turn_rate == 1.0
@test m.state == 0.0
@test m.rotational_diffusivity == 0.0
@test m.radius == 0.0
# test constructor works for all types of motility
@test_nowarn Microbe{2}(id=0, motility=RunTumble())
@test_nowarn Microbe{2}(id=0, motility=RunReverse())
@test_nowarn Microbe{2}(id=0, motility=RunReverseFlick())
# test some arguments again for 3D
id = rand(Int)
D = 3
x = rand(D) .* 500.0 |> Tuple
v = rand_vel(D) .* 40.0
mot = RunReverseFlick()
m = Microbe{D}(id=id, pos=x, vel=v, motility=mot)
@test m.id == id
@test m.pos isa NTuple{3,Float64}
@test m.pos == x
@test m.vel isa NTuple{3,Float64}
@test m.vel == v
@test m.motility isa RunReverseFlick
end
@testset "Brumley" begin
# test type hierarchy
@test Brumley{1} <: AbstractMicrobe
@test Brumley{2} <: AbstractMicrobe
@test Brumley{3} <: AbstractMicrobe
# test arguments
m = Brumley{3}(id=0)
@test m.pos isa NTuple{3,Float64}
@test m.vel isa NTuple{3,Float64}
@test m.turn_rate == 1/0.45
@test m.state == 0.0
@test m.rotational_diffusivity == 0.035
@test m.adaptation_time == 1.3
@test m.receptor_gain == 50.0
@test m.motor_gain == 50.0
@test m.chemotactic_precision == 6.0
@test m.radius == 0.5
@test m.motility isa RunReverseFlick
# default has same speed Degenerate(46.5) for forward and backward modes
@test norm(m.vel) ≈ rand(m.motility.speed_forward)
@test norm(m.vel) ≈ rand(m.motility.speed_backward)
end
@testset "Brown-Berg" begin
# test type hierarchy
@test BrownBerg{1} <: AbstractMicrobe
@test BrownBerg{2} <: AbstractMicrobe
@test BrownBerg{3} <: AbstractMicrobe
# test arguments
m = BrownBerg{3}(id=0)
@test m.pos isa NTuple{3,Float64}
@test m.vel isa NTuple{3,Float64}
@test m.turn_rate == 1/0.67
@test m.state == 0.0
@test m.rotational_diffusivity == 0.035
@test m.motor_gain == 660.0
@test m.receptor_binding_constant == 100.0
@test m.adaptation_time == 1.0
@test m.radius == 0.0
@test m.motility isa RunTumble
@test norm(m.vel) ≈ rand(m.motility.speed)
end
@testset "Celani" begin
# test type hierarchy
@test AbstractCelani <: AbstractMicrobe
@test Celani <: AbstractCelani
@test CelaniNoisy <: AbstractCelani
@test !(CelaniNoisy <: Celani)
@test !(Celani <: CelaniNoisy)
@test setdiff(fieldnames(CelaniNoisy), fieldnames(Celani)) == [:chemotactic_precision]
# test arguments
m1 = Celani{3}(id=0)
@test m1.pos isa NTuple{3,Float64}
@test m1.vel isa NTuple{3,Float64}
@test m1.turn_rate == 1/0.67
@test m1.state == [0., 0., 0., 1.]
@test m1.rotational_diffusivity == 0.26
@test m1.gain == 50.0
@test m1.memory == 1.0
@test m1.radius == 0.5
@test m1.motility isa RunTumble
@test norm(m1.vel) ≈ rand(m1.motility.speed)
m2 = CelaniNoisy{3}(id=0)
@test m2.pos isa NTuple{3,Float64}
@test m2.vel isa NTuple{3,Float64}
@test m2.turn_rate == 1/0.67
@test m2.state == [0., 0., 0., 1.]
@test m2.rotational_diffusivity == 0.26
@test m2.gain == 50.0
@test m2.memory == 1.0
@test m2.radius == 0.5
@test m2.chemotactic_precision == 1.0
@test m2.motility isa RunTumble
@test norm(m2.vel) ≈ rand(m2.motility.speed)
end
@testset "Xie" begin
# test type hierarchy
@test AbstractXie <: AbstractMicrobe
@test Xie <: AbstractXie
@test XieNoisy <: AbstractXie
@test !(XieNoisy <: Xie)
@test !(Xie <: XieNoisy)
@test setdiff(fieldnames(XieNoisy), fieldnames(Xie)) == [:chemotactic_precision]
# test arguments
m1 = Xie{3}(id=0)
@test m1.pos isa NTuple{3,Float64}
@test m1.vel isa NTuple{3,Float64}
@test m1.turn_rate_forward == 2.3
@test m1.turn_rate_backward == 1.9
@test m1.state_m == 0.0
@test m1.state_z == 0.0
@test m1.state == 0.0
@test m1.rotational_diffusivity == 0.26
@test m1.gain_forward == 2.7
@test m1.gain_backward == 1.6
@test m1.adaptation_time_m == 1.29
@test m1.adaptation_time_z == 0.28
@test m1.binding_affinity == 0.39
@test m1.radius == 0.5
@test m1.motility isa RunReverseFlick
@test m1.motility.speed_forward == m1.motility.speed_backward
m2 = XieNoisy{3}(id=0)
@test m2.pos isa NTuple{3,Float64}
@test m2.vel isa NTuple{3,Float64}
@test m2.turn_rate_forward == 2.3
@test m2.turn_rate_backward == 1.9
@test m2.state_m == 0.0
@test m2.state_z == 0.0
@test m2.state == 0.0
@test m2.rotational_diffusivity == 0.26
@test m2.gain_forward == 2.7
@test m2.gain_backward == 1.6
@test m2.adaptation_time_m == 1.29
@test m2.adaptation_time_z == 0.28
@test m2.binding_affinity == 0.39
@test m2.radius == 0.5
@test m2.chemotactic_precision == 6.0
@test m2.motility isa RunReverseFlick
@test m2.motility.speed_forward == m2.motility.speed_backward
end
end | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 4070 | using Test, Bactos, Random
@testset "Model creation" begin
timestep = 1.0
extent = 500.0
pos = Tuple(rand(3))
m = Microbe{3}(id=1, pos = pos)
microbes = [m]
# test errors
# `microbes`, `timestep` and `extent` MUST all be given
@test_throws UndefKeywordError initialise_model()
@test_throws UndefKeywordError initialise_model(;microbes)
@test_throws UndefKeywordError initialise_model(;timestep)
@test_throws UndefKeywordError initialise_model(;extent)
@test_throws UndefKeywordError initialise_model(;microbes,timestep)
@test_throws UndefKeywordError initialise_model(;microbes,extent)
@test_throws UndefKeywordError initialise_model(;timestep,extent)
model = initialise_model(;
microbes,
timestep,
extent,
random_positions = false,
)
# test default properties
@test model.properties isa Dict{Symbol,Any}
@test Set(keys(model.properties)) == Set(
(:t, :timestep, :compound_diffusivity, :concentration_field,
:concentration_gradient, :concentration_time_derivative)
)
@test model.timestep == timestep
# the model should contain the agent `m`, not a copy
@test model.agents[1] === m
# agent position should be conserved since random_positions=false
@test model.agents[1].pos == pos
model = initialise_model(;
microbes,
timestep,
extent,
random_positions = true,
)
# agent identity is still the same
@test model.agents[1] === m
# agent position is changed since random_positions=true
@test model.agents[1].pos ≠ pos
@test m.pos ≠ pos
# the new position should be inside of extent
@test all(0 .≤ model.agents[1].pos .< extent)
# if extent is a tuple, orthorhombic domains can be created
model = initialise_model(;
microbes = [Microbe{3}(id=0)], timestep,
extent = (300.0,400.0,250.0)
)
@test model.space.extent == (300.0, 400.0, 250.0)
# if extent is a scalar, the domain is cubic;
# if extent is a tuple, the domain can be orthorhombic;
# if extent has different size from microbe dimensionality,
# errors should be thrown
my_init(extent) = initialise_model(;
microbes = [Microbe{3}(id=0)],
extent,
timestep
)
@test_throws ErrorException my_init((1.0,))
@test_throws ErrorException my_init((1.0, 1.0))
@test_throws ErrorException my_init((1.0, 1.0, 1.0, 1.0))
model1 = my_init(1.0)
model2 = my_init((1.0, 2.0, 3.0))
@test model1.space.extent == (1.0, 1.0, 1.0)
@test model2.space.extent == (1.0, 2.0, 3.0)
# test mixed species models
timestep = 1.0
extent = 1.0
microbes = [Brumley{1}(id=1), Brumley{1}(id=2)]
model = initialise_model(; microbes, timestep, extent)
@test model.agents isa Dict{Int, Brumley{1}}
microbes = [Microbe{1}(id=1), Brumley{1}(id=2), Xie{1}(id=3)]
model = initialise_model(; microbes, timestep, extent)
@test model.agents isa Dict{Int, Union{Microbe{1}, Brumley{1}, Xie{1}}}
@testset "DiffEq Integrator" begin
microbes = [Microbe{1}(id=0)]
timestep = 0.1
extent = 1.0
model = initialise_model(; microbes, timestep, extent)
# simple ode: du/dt = p
# solution: u(t) = u(0) + p*t
my_ode_step!(du, u, p, t) = (du .= p[1])
u₀ = [0.0]
p = (1.0,)
integrator = initialise_ode(my_ode_step!, u₀, p)
# check integrator is initialised correctly
@test integrator.u == u₀
@test !(integrator.u === u₀)
@test integrator.p == p
@test integrator.p === p
model = initialise_model(;
microbes, timestep, extent,
model_properties = Dict(:integrator => integrator)
)
@test model.integrator === integrator
# advance ode for n steps of size timestep
n = 5
run!(model, microbe_step!, model_step!, n)
@test model.integrator === integrator
@test integrator.u[1] ≈ p[1] * timestep * n
end
end | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 2485 | using Test, Bactos, Random
using Distributions: Uniform
@testset "Motility" begin
@testset "Motile state" begin
@test instances(TwoState) == (Forward, Backward)
# call without argument chooses an instance at random
@test TwoState() ∈ instances(TwoState)
# bitwise not switches between Forward and Backward
@test ~Forward == Backward
@test ~Backward == Forward
# call to MotileState without argument chooses random state
motstate = MotileState()
@test motstate.state ∈ instances(TwoState)
# or the instance can be specified
motstate = MotileState(Forward)
@test motstate.state == Forward
end
@test AbstractMotilityOneStep <: AbstractMotility
@test AbstractMotilityTwoStep <: AbstractMotility
@test !(AbstractMotilityOneStep <: AbstractMotilityTwoStep)
@test RunTumble <: AbstractMotilityOneStep
m = RunTumble()
@test m.speed == Degenerate(30.0)
@test m.polar == Uniform(-π, π)
@test m.azimuthal == Arccos()
@test RunReverse <: AbstractMotilityTwoStep
m = RunReverse()
@test m.speed_forward == Degenerate(30.0)
@test m.polar_forward == Degenerate(π)
@test m.azimuthal_forward == Arccos()
@test m.speed_backward === m.speed_forward
@test m.polar_backward === m.polar_forward
@test m.azimuthal_backward === m.azimuthal_forward
@test m.motile_state isa MotileState
# no :state field, but due to getproperty! overload
# it directly accesses motile_state.state
@test !hasfield(RunReverse, :state)
@test m.state === m.motile_state.state
@test m.state isa TwoState
# switching motility equals to switching state
s = m.state
switch!(m)
@test m.state == ~s
# state can be set manually due to setproperty! overload
m.state = Forward
@test m.state == Forward
@test RunReverseFlick <: AbstractMotilityTwoStep
m = RunReverseFlick()
@test m.speed_forward == Degenerate(30.0)
@test m.polar_forward == Degenerate(π)
@test m.azimuthal_forward == Arccos()
@test m.speed_backward === m.speed_forward
@test m.polar_backward == [-π/2, π/2]
@test m.azimuthal_backward === m.azimuthal_forward
@test m.motile_state isa MotileState
# no :state field, but due to getproperty! overload
# it directly accesses motile_state.state
@test !hasfield(RunReverse, :state)
@test m.state === m.motile_state.state
@test m.state isa TwoState
end | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 1281 | using Test, Bactos, Random
using LinearAlgebra: norm
@testset "Pathfinder interface" begin
walkmap = BitArray(rand((0,1), 10, 10))
L = 10
extent = (L, L)
periodic = false
pathfinder1 = initialise_pathfinder(extent, periodic, walkmap)
pathfinder2 = initialise_pathfinder(L, periodic, walkmap)
# initialising with a tuple or a scalar should be the same
@test pathfinder1.dims == pathfinder2.dims
# pathfinder.walkmap should be just a reference to walkmap
@test pathfinder1.walkmap === walkmap
spherepos = (5,5)
sphereradius = 3
proberadius = 0.5
spheres = [ObstacleSphere(spherepos, sphereradius)]
Δ = proberadius # mesh resolution (defaults to proberadius/2)
walkmap = get_walkmap(extent, proberadius, spheres; Δ)
# walkmap should be false within the sphere area, true otherwise
mesh = (x = 0:Δ:L, y = 0:Δ:L)
walkmap2 = similar(walkmap)
for j in eachindex(mesh[:y]), i in eachindex(mesh[:x])
pos = (mesh[:x][i], mesh[:y][j])
# contact is allowed so if distance = radius the value is true
if norm(pos .- spherepos) < sphereradius + proberadius
walkmap2[i,j] = false
else
walkmap2[i,j] = true
end
end
@test walkmap == walkmap2
end | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 5147 | using Test, Bactos, Random
using LinearAlgebra: norm, dot
using StaticArrays
using Distributions: Uniform, Normal
@testset "Microbe reorientations" begin
≊(x,y) = isapprox(x, y, atol=1e-12) # \approxeq
@testset "One-dimensional reorientations" begin
# all reorientations in 1D should be just reversals
motility = RunTumble(speed=[1.0])
vel = (1.0,)
m = Microbe{1}(id=1; vel, motility)
turn!(m, m.motility)
@test vel == .-m.vel
turn!(m, m.motility)
@test vel == m.vel
motile_state = MotileState(Forward)
motility = RunReverseFlick(speed_forward=[1.0]; motile_state)
vel = (1.0,)
m = Microbe{1}(id=1; vel, motility)
turn!(m, m.motility)
@test vel == .-m.vel
@test motility.state == Backward
turn!(m, m.motility)
@test vel == m.vel
@test motility.state == Forward
end
@testset "Two-dimensional reorientations" begin
u = SVector(1.0, 0.0)
# a null rotation should leave u unchanged
v1 = rotate(u, 0)
@test u == v1
v2 = rotate(u, 0, 0)
@test u == v2
# 90-degree rotation
v3 = rotate(u, π/2)
@test v3 ≊ SVector(0.0, 1.0)
# azimuthal angle has no effect on 2d rotation
v4 = rotate(u, π/2, rand(Uniform(0,2π)))
@test v3 ≊ v4
v5 = rotate(u, π)
# 180-degree rotation
@test u ≊ .-v5
# rotation by multiple of 2π leave u unchanged
v6 = rotate(u, 200π)
@test u ≊ v6
U = 30.0
vel = rand_vel(2) .* U
motility = RunReverseFlick(
speed_forward = [U],
motile_state = MotileState(Forward),
polar_backward = [π/2] # exclude -π/2
)
m = Microbe{2}(id=1; vel, motility)
# 5 steps should lead back to initial orientation
# reverse (π)
turn!(m, m.motility)
@test SVector(m.vel) ≊ SVector(-vel[1], -vel[2])
# flick (π/2)
turn!(m, m.motility)
@test dot(m.vel, vel) ≊ 0
@test SVector(m.vel) ≊ SVector(vel[2], -vel[1])
# reverse (π)
turn!(m, m.motility)
@test SVector(m.vel) ≊ SVector(-vel[2], vel[1])
# flick (π/2)
turn!(m, m.motility)
@test SVector(m.vel) ≊ SVector(-vel[1], -vel[2])
# reverse (π)
turn!(m, m.motility)
@test SVector(m.vel) ≊ SVector(vel)
end
@testset "Three-dimensional reorientations" begin
U = 30.0
vel = rand_vel(3) .* U
θ = π/6
polar = [θ]
motility = RunTumble(
speed = [U],
polar = polar,
)
m = Microbe{3}(id=1; vel, motility)
turn!(m, m.motility)
@test dot(m.vel, vel)/U^2 ≊ cos(θ)
U = 30.0
vel = (U, 0.0, 0.0)
θ = π/4
φ = π/6
polar = [θ]
azimuthal = [φ]
motility = RunTumble(
speed = [U],
polar = polar,
azimuthal = azimuthal,
)
m = Microbe{3}(id=1; vel, motility)
turn!(m, m.motility)
@test SVector(m.vel) ≊ SVector(U*cos(θ), U*sin(θ)*sin(φ), -U*sin(θ)*cos(φ))
@test dot(m.vel, vel)/U^2 ≊ cos(θ)
end
@testset "Rotational diffusion" begin
dt = 1.0
vel = (1.0,)
rotational_diffusivity = 0.3
m = Microbe{1}(id=1; vel, rotational_diffusivity)
# in 1D rotational diffusion is deactivated, nothing should happen
rotational_diffusion!(m, dt)
@test m.vel == vel
dt = 1.0
rotational_diffusivity = 0.0
m = Microbe{2}(id=1; rotational_diffusivity)
vel = m.vel
rotational_diffusion!(m, dt)
# if rotational_diffusivity = 0 vel should be unchanged
@test m.vel == vel
dt = 1.0
rotational_diffusivity = 0.3
σ = sqrt(2*rotational_diffusivity*dt)
m = Microbe{2}(id=1; rotational_diffusivity)
vel = m.vel
U = norm(vel)
# fix rng state
N = 7
Random.seed!(N)
θ = rand(Normal(0,σ))
# reset rng
Random.seed!(N)
rotational_diffusion!(m, dt)
# reorientation should be of an angle θ and norm should be conserved
@test dot(m.vel, vel)/U^2 ≊ cos(θ)
# same tests for 3d
dt = 1.0
rotational_diffusivity = 0.0
m = Microbe{3}(id=1; rotational_diffusivity)
vel = m.vel
rotational_diffusion!(m, dt)
# if rotational_diffusivity = 0 vel should be (approx.) unchanged
@test all(m.vel .≊ vel)
dt = 1.0
rotational_diffusivity = 0.3
σ = sqrt(2*rotational_diffusivity*dt)
m = Microbe{3}(id=1; rotational_diffusivity)
vel = m.vel
U = norm(vel)
# fix rng state
N = 7
Random.seed!(N)
θ, φ = rand(Normal(0,σ)), rand(Arccos())
# reset rng
Random.seed!(N)
rotational_diffusion!(m, dt)
# reorientation should be of an angle θ and norm should be conserved
@test dot(m.vel, vel)/U^2 ≊ cos(θ)
end
end | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 312 | using Test, Bactos, Random
@testset "Bactos.jl Tests" begin
include("microbe_creation.jl")
include("motility.jl")
include("model_creation.jl")
include("reorientations.jl")
include("step.jl")
include("measurements.jl")
include("finite_differences.jl")
include("pathfinder.jl")
end | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | code | 777 | using Test, Bactos, Random
using LinearAlgebra: norm
using Agents: step!
@testset "Stepping" begin
@testset "Microbe stepping" begin
pos = ntuple(_ -> 0.5, 2)
vel = (-0.2, 0.6)
m = Microbe{2}(id=1, pos=pos, vel=vel, turn_rate=0.0, rotational_diffusivity=0.0)
dt = 0.1
model = initialise_model(;
timestep = dt,
microbes = [m],
extent = 1.0, periodic = true,
random_positions = false
)
step!(model, microbe_step!)
@test m.pos[1] ≈ 0.48
@test m.pos[2] ≈ 0.56
@test m.vel == vel
step!(model, microbe_step!, 9)
@test m.pos[1] ≈ 0.3
@test m.pos[2] ≈ 0.1 # periodic boundary conditions!
@test m.vel == vel
end
end | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | docs | 1031 | # Bactos.jl
[](https://github.com/mastrof/Bactos.jl/actions)
[](https://codecov.io/gh/mastrof/Bactos.jl)
[](https://mastrof.github.io/Bactos.jl/dev/)
Bactos.jl is a Julia framework for agent-based simulations of bacterial behavior, built on the amazing [Agents.jl](https://github.com/JuliaDynamics/Agents.jl)).
The package is still at an early stage of intense development.
Most of the core API should be stable for the foreseeable future, but many tweaks, improvements and additions still need to be made.
## Contribute
If you want to point out a bug, request some features or simply ask for info,
please don't hesitate to open an issue!
If you are interested in taking on a more active part in the development,
consider contacting me directly at [email protected].
I'll be happy to have a chat!
| Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | docs | 6798 | # Validation
It's important to check that our microbes behave as expected.
In this section, we compare various `Bactos.jl` functionalities against
theoretical results from the literature.
If some functionality lacks validation please open an issue.
## Velocity autocorrelation functions
The velocity autocorrelation functions for different swimming patterns have been evaluated analytically by Taktikos et al. (2013)<sup>1</sup>.
First, we will set identical parameters for all the swimmers.
For `RunReverse` and `RunReverseFlick` we will assume that the properties in the forward and backward mode are identical.
```julia
U = 30.0 # swimming speed in μm/s
τ_run = 1.0 # average unbiased run time in s
ω = 1 / τ_run # average unbiased turn rate in 1/s
Δt = 0.01 # integration timestep in s
extent = 1e4 # domain size in μm
```
We initialise three distinct populations, differing only in their motility, merge them all into a single population and initialise our model
```julia
n = 200 # number of microbes in each population
microbes_runtumble = [
Microbe{3}(id=i,
turn_rate=ω, motility=RunTumble(speed=[U])
)
for i in 1:n
]
microbes_runrev = [
Microbe{3}(id=n+i,
turn_rate=ω, motility=RunReverse(speed_forward=[U])
)
for i in 1:n
]
microbes_runrevflick = [
Microbe{3}(id=2n+i,
turn_rate=ω, motility=RunReverseFlick(speed_forward=[U])
)
for i in 1:n
]
microbes = vcat(
microbes_runtumble, microbes_runrev, microbes_runrevflick
)
model = initialise_model(;
microbes,
extent, periodic = true,
timestep = Δt
)
```
To evaluate the velocity autocorrelation functions, we only need to store the `:vel` field of the microbes during the simulation.
To get a good statistics we need simulation times that are sufficiently longer than the average run length `τ_run`.
```julia
nsteps = round(Int, 100τ_run / Δt)
adata = [:vel]
adf, = run!(model, microbe_step!, nsteps; adata)
```
We can now separate the dataframes for the three subpopulations by their motility type and evaluate their velocity autocorrelation functions using the built-in `autocorrelation` function.
For large amounts of data `autocorrelation` can take some time (O(t<sup>2</sup>n)).
```julia
adf_runtumble = filter(:id => id -> model.agents[id].motility isa RunTumble, adf)
adf_runrev = filter(:id => id -> model.agents[id].motility isa RunReverse, adf)
adf_runrevflick = filter(:id => id -> model.agents[id].motility isa RunReverseFlick, adf)
adfs = [adf_runtumble, adf_runrev, adf_runrevflick]
Φ = hcat([autocorrelation(a,:vel) for a in adfs]...)
```
The theoretical values (normalized) are given by Taktikos et al. (2013)<sup>1</sup>.
```julia
t = range(0, (nsteps-1)*Δt; step=Δt)
Φ_theoretical = hcat([
exp.(-t ./ τ_run),
exp.(-t ./ (τ_run / 2)),
(1 .- t ./ (2τ_run)) .* exp.(-t ./ τ_run),
]...)
```
Agreement between our simulation and theory is great.
```julia
plot(
xlims=(0,6τ_run), ylims=(-0.1, 1.05),
xlab="Δt / τ",
ylab="velocity autocorrelation",
)
plot!(t, Φ_theoretical, lw=2, lc=[1 2 3], label=["Run-Tumble" "Run-Reverse" "Run-Reverse-Flick"])
# slice simulation data for better visibility
scatter!(t[1:15:end], Φ[1:15:end,:] ./ U^2, m=:x, mc=[1 2 3], label=false)
hline!([0.0], lw=0.8, ls=:dash, lc=:black, lab=false)
```
## Mean-squared displacement
It's also easy to evaluate the mean-squared displacement (MSD) of our microbes during a simulation.
We will now run simulations of run-tumble bacteria using different reorientation distributions (parameterized by the average inclination angle θ), and compare the MSD as a function of θ to theoretical expectations using the well-known diffusivity formula by Lovely and Dahlquist (1975)<sup>2</sup>
```math
D = \dfrac{v^2\tau}{3(1-\alpha)}
```
where ``\alpha = \left< \cos\theta \right>`` represents the directional persistence of the trajectory.
Since ``D`` only depends on ``\left< \cos\theta \right>`` and not on the full ``P(\theta)`` distribution, we will simply use degenerate distributions ``P_i(\theta) = \delta(\theta-\bar\theta)`` for different values ``\bar\theta`` and compare the MSD estimated from our simulations to the theoretical expectation.
Taktikos et al. (2013)<sup>1</sup> provide the analytical expression for the MSD which interpolates between the short-term ballistic regime and the long-term diffusive regime:
```math
{\rm MSD}(t) = 6D\dfrac{\tau}{1-\alpha}
\left[
\dfrac{(1-\alpha)t}{\tau}-1+
{\rm exp}\left( -\dfrac{(1-\alpha)t}{\tau} \right)
\right]
```
We will setup our systems as usual and then run each simulation independently
```julia
using Distributions: Uniform
θs = [π/6, π/4, π/3, π/2, π]
U = 30.0 # swimming speed in μm/s
τ = 1.0 # average run time in s
ω = 1 / τ # average turn rate in 1/s
nmicrobes = 200
microbes = [
[
Microbe{3}(
id = n, turn_rate = ω,
motility = RunTumble(speed=[U], polar=[θ,-θ])
) for n in 1:nmicrobes
] for θ in θs
]
dt = 0.05 # s
L = 500.0 # μm
models = [
initialise_model(;
microbes = microbes[i],
timestep = dt, extent = L
) for i in eachindex(microbes)
]
nsteps = round(Int, 100τ / dt)
adata = [:pos]
adfs = [run!(model, microbe_step!, nsteps; adata)[1] for model in models]
```
We can now evaluate the MSD for each population using the `msd` function; since the simulations were performed in a periodic domain, we will need to specify the size of the domain as a keyword argument
```julia
MSD = msd.(adfs; L=L)
```
We can now slice our experimental data and plot the results.
```julia
t = (1:nsteps).*dt
logslice = round.(Int, exp10.(range(0,3,length=10)))
plot(
xlab = "Δt / τ",
ylab = "MSD / (Uτ)²",
legend = :bottomright, legendtitle = "1-α",
scale = :log10
)
scatter!(t[logslice]./τ, hcat(MSD...)[logslice,:]./(U*τ)^2,
m=:x, ms=6, msw=2, lab=false)
for i in eachindex(θs)
α = cos(θs[i])
T = τ / (1-α)
D = U^2*T / 3
dr² = @. 6*D*T * (t/T - 1 + exp(-t/T))
plot!(t./τ, dr²./(U*τ)^2, lab=round(1-α,digits=2), lc=i, lw=2)
end # for
plot!(xticks=exp10.(-1:2), yticks=exp10.(-2:2:2))
```
## References
1. Taktikos, J.; Stark, H.; Zaburdaev, V. How the Motility Pattern of Bacteria Affects Their Dispersal and Chemotaxis. PLoS ONE 2013, 8 (12), e81936. https://doi.org/10.1371/journal.pone.0081936.
2. Lovely, P.S.; Dahlquist, F.W. Statistical measures of bacterial motility and chemotaxis. Journal of Theoretical Biology 1975, 50 (2), 477-496. https://doi.org/10.1016/0022-5193(75)90094-6
| Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | docs | 1667 | # Bactos.jl
Agent-based modelling of bacterial motility and chemotaxis in Julia.
## Features
- Built on [Agents.jl](https://juliadynamics.github.io/Agents.jl/stable/)
- Bacterial motility in 1, 2 and 3 dimensions with customizable motile patterns.
- Chemotaxis with different tunable models (Brown-Berg, Brumley, Celani, Xie).
- Integration of differential equations in parallel with agent stepping via [DifferentialEquations.jl](https://diffeq.sciml.ai/stable/), using finite differences.
- Easy evaluation of quantities of interest (mean-squared displacement, autocorrelation functions...).
### Limitations
- The length of the integration timestep also sets the sensing timescale in chemotaxis models (i.e. the time over which a microbe integrates environmental signals).
- Reorientations are always assumed to be instantaneous.
- No hydrodynamic interactions.
## Future directions
- Swimming in flow fields.
- More behavioral strategies (chemokinesis, infotaxis...).
- Extended set of core functionalities (encounters, interactions...).
- Complex environments (non-spherical obstacles).
- Steric interactions and non-spherical microbes.
## Citation
If you use this package in work that leads to a publication, please cite the GitHub repository:
```
@misc{Foffi2022,
author = {Foffi, R.},
title = {Bactos.jl},
year = {2022},
publisher = {GitHub},
journal = {GitHub repository},
howpublished = {\url{https://github.com/mastrof/Bactos.jl}}
}
```
## Acknowledgements
This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 955910. | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.0.1 | 8f2697805b334b06f4680f13d76453ccb590c77d | docs | 7299 | # Tutorial
Ready-to-run scripts for the functionalities introduced here can be found in the `examples` directory of the [repo](https://github.com/mastrof/Bactos.jl).
## Creating a bacterium
Bacteria are represented by custom types, that must be subtypes of the `AbstractAgent` type implemented by Agents.jl.
```@docs
AbstractMicrobe
```
By default, `Bactos.jl` provides a basic `Microbe` type, that is usually sufficient for the simplest types of simulations.
```@docs
Microbe
```
In order to create a `Microbe` living in a one-dimensional space we can just call
```julia
Microbe{1}(id=0)
```
It is *required* to pass a value to the `id` argument (this behavior might change in the future).
All the other parameters will be given default values (as described in the type docstring) if not assigned explicitly.
Similarly, for bacteria living in two or three dimensions we can use
```julia
Microbe{2}(id=0)
Microbe{3}(id=0)
```
Custom parameters can be set via kwargs:
```julia
Microbe{3}(
id = 0,
pos = (300.0, 0.0, 0.0),
motility = RunTumble(speed = Normal(40.0, 4.0)),
vel = rand_vel(3) .* 40.0,
turn_rate = 1.5,
state = 0.0,
rotational_diffusivity = 0.035,
radius = 0.5
)
```
## Creating a model
BacteriaBasedModel provides a fast way to initialise an `AgentBasedModel` (from Agents.jl) via the
`initialise_model` function, using a typical procedure.
If higher levels of customization are needed, the model will need to be created by hand.
```@docs
initialise_model
```
We can now generate a population of microbes and, after choosing an integration timestep and a domain size, we initialise our model, placing the microbes at random locations in the domain.
```julia
microbes = [Microbe{3}(id=i) for i in 1:10]
timestep = 0.1
extent = 100.0
model = initialise_model(;
microbes = microbes,
timestep = timestep,
extent = extent
)
```
```
AgentBasedModel with 10 agents of type Microbe
space: periodic continuous space with (100.0, 100.0, 100.0) extent and spacing=5.0
scheduler: fastest
properties: timestep
```
## Random walks
Now we can already generate random walks.
The setup follows previous sections.
```julia
timestep = 0.1
extent = 1e6 # just a large value to stay away from boundaries
nmicrobes = 8
# initialise all microbes at same position
microbes = [Microbe{1}(id=i, pos=(L/2,)) for i in 1:nmicrobes]
model = initialise_model(;
microbes,
timestep,
extent, periodic = false,
random_positions = false
)
```
Now we need to define the `adata` variable to choose what observables we want to track, throughout the simulation, for each agent in the system. In our case, only the position field
```julia
adata = [:pos]
```
Now we can run the simulation; the `microbe_step!` function will take care of the stepping and reorientations according to the properties of each microbe:
```julia
nsteps = 1000
adf, = run!(model, microbe_step!, nsteps; adata)
```
```julia
x = first.(vectorize_adf_measurement(adf, :pos))'
plot(
(0:nsteps).*dt, x,
legend = false,
xlab = "time",
ylab = "position"
)
```
Similarly for a two-dimensional random walk, using run-reverse-flick motility and non-zero rotational diffusion:
```julia
dt = 0.1
L = 1000.0
nmicrobes = 1
microbes = [
Microbe{2}(
id=i, pos=(L/2,L/2),
motility=RunReverseFlick(),
rotational_diffusivity = 0.2,
) for i in 1:nmicrobes
]
model = initialise_model(;
microbes,
timestep = dt,
extent, periodic = false,
random_positions = false,
)
nsteps = 500
adata = [:pos]
adf, = run!(model, microbe_step!, nsteps; adata)
traj = vectorize_adf_measurement(adf, :pos)
x = first.(traj)'
y = last.(traj)'
plot(
x, y, line_z = (0:nsteps).*dt,
legend=false,
xlab = "x", ylab = "y",
colorbar = true, colorbar_title = "time"
)
```
Microbes with different motile patterns can also be combined in the same simulation, without extra complications or computational costs:
```julia
n = 3
microbes_runtumble = [Microbe{2}(id=i, motility=RunTumble()) for i in 1:n]
microbes_runrev = [Microbe{2}(id=n+i, motility=RunReverse()) for i in 1:n]
microbes_runrevflick = [Microbe{2}(id=2n+1, motility=RunReverseFlick()) for i in 1:n]
microbes = vcat(
microbes_runtumble, microbes_runrev, microbes_runrevflick
)
```
## Chemotaxis in a linear gradient
We will now reproduce a classical chemotaxis assay: bacteria in a rectangular channel with a linear attractant gradient.
`Bactos.jl` requires three functions to be defined for the built-in chemotaxis models to work: `concentration_field`, `concentration_gradient`, and `concentration_time_derivative`; all three need to take the two arguments `(pos, model)`.
First we need to define our concentration field and its gradient (we don't define its time derivative since it will be held constant). We will use a linear gradient in the `x` direction.
Here we can define also the gradient analytically, in more complex cases it can be evaluated numerically through the finite difference interface.
```julia
concentration_field(x,y,C₀,∇C) = C₀ + ∇C*x
function concentration_field(pos, model)
x, y = pos
C₀ = model.C₀
∇C = model.∇C
concentration_field(x, y, C₀, ∇C)
end
concentration_gradient(x,y,C₀,∇C) = [∇C, 0.0]
function concentration_gradient(pos, model)
x, y = pos
C₀ = model.C₀
∇C = model.∇C
concentration_gradient(x, y, C₀, ∇C)
end
```
We choose the parameters, initialise the population (with two distinct chemotaxers) with all bacteria to the left of the channel, and setup the model providing the functions for our concentration field to the `model_properties` dictionary.
```julia
timestep = 0.1 # s
Lx, Ly = 1000.0, 500.0 # μm
extent = (Lx, Ly) # μm
periodic = false
n = 50
microbes_brumley = [
Brumley{2}(id=i, pos=(0,rand()*Ly), chemotactic_precision=1)
for i in 1:n
]
microbes_brown = [
BrownBerg{2}(id=n+i, pos=(0,rand()*Ly))
for i in 1:n
]
microbes = [microbes_brumley; microbes_brown]
C₀ = 0.0 # μM
∇C = 0.01 # μM/μm
model_properties = Dict(
:concentration_field => concentration_field,
:concentration_gradient => concentration_gradient,
:concentration_time_derivative => (_,_) -> 0.0,
:compound_diffusivity => 500.0, # μm²/s
:C₀ => C₀,
:∇C => ∇C,
)
model = initialise_model(;
microbes,
timestep,
extent, periodic,
model_properties,
random_positions = false
)
```
Notice that we also defined an extra property `compound_diffusivity`. This quantity is *required* by the models of chemotaxis that use sensing noise (such as `Brumley`, `XieNoisy`, `CelaniNoisy`). `500 μm²/s` is a typical value for small molecules.
We can run the simulation as usual and extract the trajectories.
```julia
adata = [:pos]
nsteps = 1000 # corresponds to 100s
adf, = run!(model, microbe_step!, nsteps; adata)
traj = vectorize_adf_measurement(adf, :pos)
x = first.(traj)'
y = last.(traj)'
```
Comparing the trajectories for the two bacterial species we witness a chemotactic race (`Brumley` in blue, `BrownBerg` in orange).
 | Bactos | https://github.com/mastrof/Bactos.jl.git |
|
[
"MIT"
] | 0.14.3 | 9aee830051af43009b3c97651f124246fdabb86a | code | 540 | using Documenter
push!(LOAD_PATH, "../../src")
using StipplePlotly, StipplePlotly.Charts
makedocs(
sitename = "StipplePlotly - plotting library for Stipple",
format = Documenter.HTML(prettyurls = false),
warnonly = true,
pages = [
"Home" => "index.md",
"StipplePlotly API" => [
"Charts" => "API/charts.md",
"Layouts" => "API/layouts.md",
"StipplePlotly" => "API/stippleplotly.md",
]
],
)
deploydocs(
repo = "github.com/GenieFramework/StipplePlotly.jl.git",
)
| StipplePlotly | https://github.com/GenieFramework/StipplePlotly.jl.git |
|
[
"MIT"
] | 0.14.3 | 9aee830051af43009b3c97651f124246fdabb86a | code | 2137 | module StipplePlotlyPlotlyBaseExt
using StipplePlotly
using StipplePlotly.Stipple
using StipplePlotly.Charts
import Stipple.stipple_parse
isdefined(Base, :get_extension) ? (using PlotlyBase) : (using ..PlotlyBase)
function Base.Dict(p::PlotlyBase.Plot)
Dict(
:data => p.data,
:layout => p.layout,
:frames => p.frames,
:config => p.config
)
end
function PlotlyBase.Plot(d::AbstractDict)
sd = PlotlyBase._symbol_dict(d)
data = haskey(sd, :data) && ! isempty(sd[:data]) ? PlotlyBase.GenericTrace.(sd[:data]) : PlotlyBase.GenericTrace[]
layout = haskey(sd, :layout) ? PlotlyBase.Layout(sd[:layout]) : PlotlyBase.Layout()
frames = haskey(sd, :frames) && ! isempty(sd[:frames]) ? PlotlyBase.PlotlyFrame.(sd[:frames]) : PlotlyBase.PlotlyFrame[]
config = haskey(sd, :config) ? PlotlyBase.PlotConfig(; sd[:config]...) : PlotlyBase.PlotConfig()
PlotlyBase.Plot(data, layout, frames; config)
end
function Stipple.stipple_parse(::Type{PlotlyBase.Plot}, d::AbstractDict)
PlotlyBase.Plot(d)
end
function Stipple.stipple_parse(::Type{Plot{TT, TL, TF}}, d::AbstractDict) where {TT, TL, TF}
Plot{TT, TL, TF}(
stipple_parse(TT, get(d, "data", get(d, :data, GenericTrace[]))),
stipple_parse(TL, get(d, "layout", get(d, :layout, PlotlyBase.Layout()))),
stipple_parse(TF, get(d, "frames", get(d, :frames, PlotlyBase.PlotlyFrame[]))),
PlotlyBase.uuid4(),
stipple_parse(PlotlyBase.PlotConfig, get(d, "config", get(d, :config, PlotlyBase.PlotConfig())))
)
end
function Stipple.stipple_parse(::Type{T}, d::AbstractDict) where T <: PlotlyBase.AbstractTrace
T === PlotlyBase.AbstractTrace ? GenericTrace(d) : T(d)
end
function Stipple.stipple_parse(T::Type{PlotlyBase.GenericTrace{D}}, d::AbstractDict) where D <: AbstractDict
T(stipple_parse(D, PlotlyBase._symbol_dict(d)))
end
function Stipple.stipple_parse(::Type{PlotlyBase.Layout}, d::AbstractDict)
PlotlyBase.Layout(d)
end
function Stipple.stipple_parse(::Type{PlotlyBase.Layout{D}}, d::AbstractDict) where D
PlotlyBase.Layout(stipple_parse(D, PlotlyBase._symbol_dict(d)))
end
end | StipplePlotly | https://github.com/GenieFramework/StipplePlotly.jl.git |
|
[
"MIT"
] | 0.14.3 | 9aee830051af43009b3c97651f124246fdabb86a | code | 39479 | module Charts
using Genie, Stipple, StipplePlotly
using Stipple.Reexport, Stipple.ParsingTools
import Stipple: stipple_parse
import StipplePlotly._symbol_dict
import DataFrames
include("Layouts.jl")
using .Layouts
@reexport using .Layouts:PlotLayoutMapbox, MCenter, GeoProjection, PRotation,
PlotLayoutGeo, PlotLayout, PlotAnnotation, ErrorBar, Font,
ColorBar, PlotLayoutGrid, PlotLayoutAxis, PlotLayoutTitle, PlotLayoutLegend
using .Layouts:optionals!
import Genie.Renderer.Html: HTMLString, normal_element, register_normal_element
export PlotLayout, PlotData, PlotAnnotation, Trace, plot, ErrorBar, Font, ColorBar, watchplot, watchplots
export PlotLayoutGrid, PlotLayoutAxis
export PlotConfig, PlotLayoutTitle, PlotLayoutLegend, PlotlyLine, PlotDataMarker
export PlotlyEvents, PlotWithEvents, PlotWithEventsReadOnly
export plotdata
const PLOT_TYPE_LINE = "scatter"
const PLOT_TYPE_SCATTER = "scatter"
const PLOT_TYPE_SCATTERGL = "scattergl"
const PLOT_TYPE_SCATTERGEO = "scattergeo"
const PLOT_TYPE_SCATTERMAPBOX = "scattermapbox"
const PLOT_TYPE_BAR = "bar"
const PLOT_TYPE_PIE = "pie"
const PLOT_TYPE_HEATMAP = "heatmap"
const PLOT_TYPE_HEATMAPGL = "heatmapgl"
const PLOT_TYPE_IMAGE = "image"
const PLOT_TYPE_CONTOUR = "contour"
const PLOT_TYPE_CHOROPLETH = "choropleth"
# const PLOT_TYPE_CHOROPLETHMAPBOX = "choroplethmapbox"
const PLOT_TYPE_TABLE = "table"
const PLOT_TYPE_BOX = "box"
const PLOT_TYPE_VIOLIN = "violin"
const PLOT_TYPE_HISTOGRAM = "histogram"
const PLOT_TYPE_HISTOGRAM2D = "histogram2d"
const PLOT_TYPE_HISTOGRAM2DCONTOUR = "histogram2dcontour"
const PLOT_TYPE_OHLC = "ohlc"
const PLOT_TYPE_CANDLESTICK = "candlestick"
const PLOT_TYPE_WATERFALL = "waterfall"
const PLOT_TYPE_FUNNEL = "funnel"
const PLOT_TYPE_FUNNELAREA = "funnelarea"
const PLOT_TYPE_INDICATOR = "indicator"
const PLOT_TYPE_SCATTER3D = "scatter3d"
const PLOT_TYPE_SURFACE = "surface"
const PLOT_TYPE_MESH3D = "mesh3d"
const PLOT_TYPE_CONE = "cone"
const PLOT_TYPE_STREAMTUBE = "streamtube"
const PLOT_TYPE_VOLUME = "volume"
const PLOT_TYPE_ISOSURFACE = "isosurface"
const PLOT_TYPE_TIMELINE = "timeline"
const DEFAULT_CONFIG_TYPE = Ref{DataType}()
const PB_PKGID = Base.PkgId(Base.UUID("a03496cd-edff-5a9b-9e67-9cda94a718b5"), "PlotlyBase")
kebapcase(s::String) = lowercase(replace(s, r"([A-Z])" => s"-\1"))
kebapcase(s::Symbol) = Symbol(kebapcase(String(s)))
register_normal_element("plotly", context = @__MODULE__)
function __init__()
DEFAULT_CONFIG_TYPE[] = Charts.PlotConfig
end
function default_config_type()
if DEFAULT_CONFIG_TYPE[] == Charts.PlotConfig
pkg = get(Base.loaded_modules, PB_PKGID, nothing)
if pkg !== nothing
DEFAULT_CONFIG_TYPE[] = pkg.PlotConfig
end
end
DEFAULT_CONFIG_TYPE[]
end
"""
function plotly(p::Symbol; layout = Symbol(p, ".layout"), config = Symbol(p, ".config"), configtype = default_config_type(), keepselection = false, kwargs...)
This is a convenience function for rendering a PlotlyBase.Plot or a struct with fields data, layout and config
# Example
```julia
julia> plotly(:plot)
"<plotly :data=\"plot.data\" :layout=\"plot.layout\" :config=\"plot.config\"></plotly>"
```
For multiple plots with a common config or layout a typical usage is
```julia
julia> plotly(:plot, config = :config)
"<plotly :data=\"plot.data\" :layout=\"plot.layout\" :config=\"config\"></plotly>"
```
"""
function plotly(p::Symbol, args...; layout = Symbol(p, ".layout"), config = Symbol(p, ".config"), configtype = default_config_type(), keepselection = false, kwargs...)
plot("$p.data", args...; layout, config, configtype, keepselection, kwargs...)
end
"""
function watchplot(selector::AbstractString)
Generates a js script that forwards plotly events of a DOM element to its respective model fields,
e.g. `plot_selected`, `plot_hover`, etc...
If no prefix is given, it is taken from the class list which needs to contain at least one entry `'sync_[prefix]'`, e.g `sync_plot`.
This function acts on plots that are already present in the UI. It is meant for the rare case of
plot-specific event-binding, e.g. in a backend listener.
The normal way forwarding plot events is to call `watchplots()` in `js_mounted()`.
"""
function watchplot(selector::AbstractString)
"window.watchPlot(document.querySelector('$selector'), this, $prefix)\n"
end
function watchplot(selector::AbstractString, prefix)
"window.watchGraphDiv(document.querySelector('$selector'), this, $prefix)\n"
end
"""
function watchplot(id::Symbol)
Call watchplot with an 'id' instead of a CSS selector string.
"""
function watchplot(id::Symbol)
"window.watchPlot(document.getElementById('$id'), this)\n"
end
"""
function watchplots(model = "this"; observe = true, parentSelector::Union{Nothing, AbstractString} = nothing)
Generates a js script that forwards plotly events, e.g. point selection or hovering, to their respective model fields.
`model` can be a string, a model or a model type. Dynamically added plots are also covered.
The recommended usage is to called it on the mounted event. In that case the model argument can be omitted.
`Stipple.js_mounted(::Example) = watchplots()`
Plots to be covered by this approach must contain at least one class entry `'sync_[prefix]'`, e.g `sync_plot`.
You can use the keyword arguments `syncevents` or `syncprefix` of `plot()` to generate the UI plot nodes:
```
julia> plot("plot.data", syncevents = true)
"<plotly :data=\"plot.data\" :layout=\"{}\" class=\"sync_plot\"></plotly>"
julia> plot("plot.data", syncprefix = "plot1")
"<plotly :data=\"plot.data\" :layout=\"{}\" class=\"sync_plot1\"></plotly>"
```
# Example
```julia
@vars Example begin
plot::R{Plot} = Plot()
plot_selected::R{Dict{String, Any}} = Dict{String, Any}()
plot_hover::R{Dict{String, Any}} = Dict{String, Any}()
plot1_selected::R{Dict{String, Any}} = Dict{String, Any}()
end
function ui(model::Example)
page(model, class = "container",
row(cell(class = "st-module", id = "plotcontainer", [
# syncs plotly events to field plot_selected, plot_hover, etc...
plotly(:plot, syncevents = true),
# syncs plotly events to field plot1_selected, plot1_hover, etc...
plotly(:plot, syncprefix = "plot1", @iif(length(model.plot.data) > 0)),
])))
end
Stipple.js_mounted(::Example) = watchplots()
function handlers(model)
on(model.isready) do isready
isready || return
push!(model)
end
on(model.plot_selected) do data
haskey(data, "points") && @info "Selection: \$(getindex.(data["points"], "pointIndex"))"
end
return model
end
```
"""
function watchplots(model::Union{Symbol, AbstractString} = "this"; observe = true, parentSelector::Union{Nothing, AbstractString} = nothing)
"""watchPlots($model, $observe, $(isnothing(parentSelector) ? "''" : parentSelector))\n"""
end
function watchplots(model::Union{M, Type{M}}; observe = true,
parentSelector::Union{Nothing, AbstractString} = nothing) where M <: ReactiveModel
watchplots(vm(model); observe, parentSelector)
end
Base.@kwdef mutable struct PlotlyLine
# for all Plotly lines:
color::Union{String,Nothing} = nothing
width::Union{Int,Nothing} = nothing # 2
# Scatter - line:
shape::Union{String,Nothing} = nothing # "linear" | "spline" | "hv" | "vh" | "hvh" | "vhv"
smoothing::Union{Float64,String,Nothing} = nothing
dash::Union{String,Nothing} = nothing # "solid", "dot", "dash", "longdash", "dashdot", "longdashdot" or "5px,10px,2px,2px"
simplify::Union{Bool,Nothing} = nothing
# Scatter - marker - line:
cauto::Union{Bool,Nothing} = nothing
cmin::Union{Float64,Nothing} = nothing
cmax::Union{Float64,Nothing} = nothing
cmid::Union{Float64,Nothing} = nothing
colorscale::Union{Matrix,String,Nothing} = nothing
autocolorscale::Union{Bool,Nothing} = nothing
reversescale::Union{Bool,Nothing} = nothing
# Box - marker - line
outliercolor::Union{String,Nothing} = nothing
outlierwidth::Union{Int,Nothing} = nothing # 1
end
function Base.show(io::IO, pdl::PlotlyLine)
output = "Layout Legend: \n"
for f in fieldnames(typeof(pdl))
prop = getproperty(pdl, f)
if prop !== nothing
output *= "$f = $prop \n"
end
end
print(io, output)
end
function Base.Dict(pdl::PlotlyLine)
trace = Dict{Symbol, Any}()
optionals!(trace, pdl, [:color, :width, :shape, :smoothing, :dash, :simplify, :cauto, :cmin, :cmax, :cmid, :colorscale, :autocolorscale, :reversescale, :outliercolor, :outlierwidth])
end
function Stipple.render(pdl::PlotlyLine, fieldname::Union{Symbol,Nothing} = nothing)
Dict(pdl)
end
#===#
"""
PlotDataMarker()
----------
# Examples
----------
```
julia> marker = PlotDataMarker(
size = [20, 30, 15, 10],
color = [10.0, 20.0, 40.0, 50.0],
cmin = 0.0,
cmax = 50.0,
colorscale = "Greens",
colorbar = ColorBar(title_text = "Some rate", ticksuffix = "%", showticksuffix = "last"),
line = PlotlyLine(color = "black")
)
```
-----------
# Properties
-----------
* `autocolorscale::Bool` - Determines whether the colorscale is a default palette (`autocolorscale: true`) or the palette determined by `marker.colorscale`. Has an effect only if in `marker.color` is set to a numerical array. In case `colorscale` is unspecified or `autocolorscale` is true, the default palette will be chosen according to whether numbers in the `color` array are all positive, all negative or mixed. Default: `true`
* `cauto::Bool` - Determines whether or not the color domain is computed with respect to the input data (here in `marker.color`) or the bounds set in `marker.cmin` and `marker.cmax` Has an effect only if in `marker.color` is set to a numerical array. Defaults to `false` when `marker.cmin` and `marker.cmax` are set by the user.
* `cmax::Float64,Nothing` - Sets the upper bound of the color domain. Has an effect only if in `marker.color` is set to a numerical array. Value should have the same units as in `marker.color` and if set, `marker.cmin` must be set as well.
* `cmin::Float64` - Sets the mid-point of the color domain by scaling `marker.cmin` and/or `marker.cmax` to be equidistant to this point. Has an effect only if in `marker.color` is set to a numerical array. Value should have the same units as in `marker.color`. Has no effect when `marker.cauto` is `false`.
* `color::Union{String,Vector{Float64}}` - Sets the marker color. It accepts either a specific color or an array of numbers that are mapped to the colorscale relative to the max and min values of the array or relative to `marker.cmin` and `marker.cmax` if set.
* `coloraxis::String` - Sets a reference to a shared color axis. References to these shared color axes are "coloraxis", "coloraxis2", "coloraxis3", etc. Settings for these shared color axes are set in the layout, under `layout.coloraxis`, `layout.coloraxis2`, etc. Note that multiple color scales can be linked to the same color axis.
* `colorbar::ColorBar` - ColorBar object contains multiple keys. Check correspoing API docs for each key. ex. `ColorBar(title_text = "Some rate", ticksuffix = "%", showticksuffix = "last")`
* `colorscale::Union{Matrix,String}` - Sets the colorscale. Has an effect only if in `marker.color` is set to a numerical array. The colorscale must be an array containing arrays mapping a normalized value to an rgb, rgba, hex, hsl, hsv, or named color string. At minimum, a mapping for the lowest (0) and highest (1) values are required. For example, `[[0, 'rgb(0,0,255)'], [1, 'rgb(255,0,0)']]`. To control the bounds of the colorscale in color space, use `marker.cmin` and `marker.cmax`. Alternatively, `colorscale` may be a palette name string of the following list: Blackbody,Bluered,Blues,Cividis,Earth,Electric,Greens,Greys,Hot,Jet,Picnic,Portland,Rainbow,RdBu,Reds,Viridis,YlGnBu,YlOrRd.
* `line::PlotlyLine` - object contains multiple keys. Check correspoing API docs for each key. ex. `PlotlyLine(color = "black", width = 2)`
* `opacity::Union{Float64, Vector{Float64}}` - Sets the marker opacity. Type. number or array of numbers between or equal to 0 and 1
* `reversescale::Bool` - Reverses the color mapping if true. Has an effect only if in `marker.color` is set to a numerical array. If true, `marker.cmin` will correspond to the last color in the array and `marker.cmax` will correspond to the first color.
* `showscale::Bool` - Determines whether or not a colorbar is displayed for this trace. Has an effect only if in `marker.color` is set to a numerical array.
* `size::Union{Int,Vector{Int}}` - Sets the marker size (in px).
* `sizemin::Float64` - Has an effect only if `marker.size` is set to a numerical array. Sets the minimum size (in px) of the rendered marker points.
* `sizemode::String` - Has an effect only if `marker.size` is set to a numerical array. Sets the rule for which the data in `size` is converted to pixels.
* `sizeref::Float64` - Has an effect only if `marker.size` is set to a numerical array. Sets the scale factor used to determine the rendered size of marker points. Use with `sizemin` and `sizemode`.
* `symbol::Union{String, Vector{String}}` - Sets the marker symbol type. Adding 100 is equivalent to appending "-open" to a symbol name. Adding 200 is equivalent to appending "-dot" to a symbol name. Adding 300 is equivalent to appending "-open-dot" or "dot-open" to a symbol name. Ex. Default: "circle"
"""
Base.@kwdef mutable struct PlotDataMarker
autocolorscale::Union{Bool,Nothing} = nothing
cauto::Union{Bool,Nothing} = nothing
cmax::Union{Float64,Nothing} = nothing
cmid::Union{Float64,Nothing} = nothing
cmin::Union{Float64,Nothing} = nothing
# TODO: gradient
color::Union{String,Vector{Float64},Nothing} = nothing # color= [2.34, 4.3, 34.5, 52.2]
# Specific for Pie charts:
colors::Union{Vector{String},Nothing} = nothing
coloraxis::Union{String,Nothing} = nothing
colorbar::Union{ColorBar,Nothing} = nothing
colorscale::Union{Matrix,String,Nothing} = nothing
line::Union{PlotlyLine,Nothing} = nothing
maxdisplayed::Union{Int,Nothing} = nothing
opacity::Union{Float64,Vector{Float64},Nothing} = nothing
reversescale::Union{Bool,Nothing} = nothing
showscale::Union{Bool,Nothing} = nothing
size::Union{Int,Vector{Int},Nothing} = nothing
sizemin::Union{Float64,Nothing} = nothing
sizemode::Union{String,Nothing} = nothing
sizeref::Union{Float64,Nothing} = nothing
symbol::Union{String,Vector{String},Nothing} = nothing
end
function Base.show(io::IO, pdm::PlotDataMarker)
output = "Layout Legend: \n"
for f in fieldnames(typeof(pdm))
prop = getproperty(pdm, f)
if prop !== nothing
output *= "$f = $prop \n"
end
end
print(io, output)
end
function Base.Dict(pdm::PlotDataMarker)
trace = Dict{Symbol, Any}()
(pdm.line !== nothing) && (trace[:line] = Dict(pdm.line))
(pdm.colorbar !== nothing) && (trace[:colorbar] = Dict(pdm.colorbar))
optionals!(trace, pdm, [
:autocolorscale, :cauto, :cmax, :cmid, :cmin, :color, :colors, :coloraxis,
:colorbar, :colorscale, :line, :maxdisplayed, :opacity, :reversescale,
:showscale, :size, :sizemin, :sizemode, :sizeref, :symbol])
end
function Stipple.render(pdm::PlotDataMarker, fieldname::Union{Symbol,Nothing} = nothing)
Dict(pdm)
end
#===#
Base.@kwdef mutable struct PlotData
plot::String = PLOT_TYPE_SCATTER
align::Union{String,Nothing} = nothing
alignmentgroup::Union{String,Nothing} = nothing
alphahull::Union{Int,Float64,Nothing} = nothing
anchor::Union{String,Nothing} = nothing
aspectratio::Union{Float64,Int,Nothing} = nothing
autobinx::Union{Bool,Nothing} = nothing
autobiny::Union{Bool,Nothing} = nothing
autocolorscale::Union{Bool,Nothing} = nothing
autocontour::Union{Bool,Nothing} = nothing
automargin::Union{Bool,Nothing} = nothing
bandwidth::Union{Float64,Int,Nothing} = nothing
base::Union{Vector,Float64,Int,String,Nothing} = nothing
baseratio::Union{Float64,Int,Nothing} = nothing
bingroup::Union{String,Nothing} = nothing
box::Union{Dict,Nothing} = nothing
boxmean::Union{Bool,String,Nothing} = nothing
boxpoints::Union{Bool,String,Nothing} = nothing
caps::Union{Dict,Nothing} = nothing
cauto::Union{Bool,Nothing} = nothing
cells::Union{Dict,Nothing} = nothing
cliponaxis::Union{Bool,Nothing} = nothing
close::Union{Vector,Nothing} = nothing
cmax::Union{Float64,Int,Nothing} = nothing
cmid::Union{Float64,Int,Nothing} = nothing
cmin::Union{Float64,Int,Nothing} = nothing
color::Union{String,Nothing} = nothing
coloraxis::Union{String,Nothing} = nothing
colorbar::Union{Dict,ColorBar,Nothing} = nothing
colorscale::Union{Matrix,String,Nothing} = nothing
columnorder::Union{Vector,Nothing} = nothing
columnwidth::Union{Float64,Int,Vector,Nothing} = nothing
connectgaps::Union{Bool,Nothing} = nothing
connector::Union{Dict,Nothing} = nothing
constraintext::Union{String,Nothing} = nothing
contour::Union{Dict,Nothing} = nothing
contours::Union{Dict,Nothing} = nothing
cumulative::Union{Dict,Nothing} = nothing
customdata::Union{Vector,Nothing} = nothing
decreasing::Union{Dict,Nothing} = nothing
delaunayaxis::Union{Char,String,Nothing} = nothing
delta::Union{Dict,Nothing} = nothing
direction::Union{String,Nothing} = nothing
dlabel::Union{Int,Nothing} = nothing
domain::Union{Dict,Nothing} = nothing
dx::Union{Int,Nothing} = nothing
dy::Union{Int,Nothing} = nothing
error_x::Union{Dict,ErrorBar,Nothing} = nothing
error_y::Union{Dict,ErrorBar,Nothing} = nothing
error_z::Union{Dict,ErrorBar,Nothing} = nothing
facecolor::Union{Vector,Nothing} = nothing
fill::Union{String,Nothing} = nothing
fillcolor::Union{String,Nothing} = nothing
flatshading::Union{Bool,Nothing} = nothing
gauge::Union{Dict,Nothing} = nothing
geojson::Union{String,Nothing} = nothing
groupnorm::Union{String,Nothing} = nothing
header::Union{Dict,Nothing} = nothing
hidesurface::Union{Bool,Nothing} = nothing
high::Union{Vector,Nothing} = nothing
histfunc::Union{String,Nothing} = nothing
histnorm::Union{String,Nothing} = nothing
hole::Union{Float64,Nothing} = nothing
hovertext::Union{Vector{String},String,Nothing} = nothing
hoverinfo::Union{String,Nothing} = nothing
hoverlabel::Union{Dict,Nothing} = nothing
hoveron::Union{String,Nothing} = nothing
hoverongaps::Union{Bool,Nothing} = nothing
hovertemplate::Union{Vector{String},String,Nothing} = nothing
i::Union{Vector,Nothing} = nothing
intensity::Union{Vector,Nothing} = nothing
intensitymode::Union{String,Nothing} = nothing
j::Union{Vector,Nothing} = nothing
k::Union{Vector,Nothing} = nothing
ids::Union{Vector{String},Nothing} = nothing
increasing::Union{Dict,Nothing} = nothing
insidetextanchor::Union{String,Nothing} = nothing
insidetextfont::Union{Font,Nothing} = nothing
insidetextorientation::Union{String,Nothing} = nothing
isomax::Union{Float64,Int,Nothing} = nothing
isomin::Union{Float64,Int,Nothing} = nothing
jitter::Union{Float64,Nothing} = nothing
labels::Union{Vector,Nothing} = nothing
label0::Union{Int,Nothing} = nothing
lat::Union{Vector,Nothing} = nothing
legendgroup::Union{String,Nothing} = nothing
lighting::Union{Dict,Nothing} = nothing
lightposition::Union{Dict,Nothing} = nothing
line::Union{Dict,PlotlyLine,Nothing} = nothing
locations::Union{Vector,Nothing} = nothing
locationmode::Union{String,Nothing} = nothing
lon::Union{Vector,Nothing} = nothing
low::Union{Vector,Nothing} = nothing
lowerfence::Union{Vector,Nothing} = nothing
marker::Union{Dict,PlotDataMarker,Nothing} = nothing
maxdisplayed::Union{Int,Nothing} = nothing
mean::Union{Vector,Nothing} = nothing
measure::Union{Vector,Nothing} = nothing
meanline::Union{Dict,Nothing} = nothing
median::Union{Vector,Nothing} = nothing
meta::Union{Float64,Int,String,Nothing} = nothing
mode::Union{String,Nothing} = nothing
name::Union{String,Nothing} = nothing
nbinsx::Union{Int,Nothing} = nothing
nbinsy::Union{Int,Nothing} = nothing
ncontours::Union{Int,Nothing} = nothing
notched::Union{Bool,Nothing} = nothing
notchwidth::Union{Float64,Nothing} = nothing
notchspan::Union{Vector,Nothing} = nothing
number::Union{Dict,Nothing} = nothing
offset::Union{Float64,Int,Vector,Nothing} = nothing
offsetgroup::Union{String,Nothing} = nothing
opacity::Union{Float64,Nothing} = nothing
opacityscale::Union{Float64,Int,Vector,String,Nothing} = nothing
colormodel::Union{String,Nothing} = nothing # image trace color models: "rgb" | "rgba" | "rgba256" | "hsl" | "hsla"
open::Union{Vector,Nothing} = nothing
orientation::Union{String,Nothing} = nothing
outsidetextfont::Union{Font,Nothing} = nothing
points::Union{Bool,String,Nothing} = nothing
pointpos::Union{Float64,Nothing} = nothing
projection::Union{Dict,Nothing} = nothing
pull::Union{Float64,Vector,Nothing} = nothing
q1::Union{Vector,Nothing} = nothing
q3::Union{Vector,Nothing} = nothing
quartilemethod::Union{String,Nothing} = nothing
reversescale::Union{Bool,Nothing} = nothing
rotation::Union{Int,Nothing} = nothing
scalegroup::Union{String,Nothing} = nothing
scalemode::Union{String,Nothing} = nothing
scene::Union{String,Nothing} = nothing
sd::Union{Vector,Nothing} = nothing
selected::Union{Dict,Nothing} = nothing
selectedpoints::Union{Vector{<:Integer},Float64,Int,String,Nothing} = nothing
showlegend::Union{Bool,Nothing} = nothing
showscale::Union{Bool,Nothing} = nothing
side::Union{String,Nothing} = nothing
sizemode::Union{String,Nothing} = nothing
sizeref::Union{Float64,Int,Nothing} = nothing
slices::Union{Dict,Nothing} = nothing
sort::Union{Bool,Nothing} = nothing
source::Union{String,Nothing} = nothing
spaceframe::Union{Dict,Nothing} = nothing
span::Union{Vector,Nothing} = nothing
spanmode::Union{String,Nothing} = nothing
stackgaps::Union{String,Nothing} = nothing
stackgroup::Union{String,Nothing} = nothing
starts::Union{Dict,Nothing} = nothing
surface::Union{Dict,Nothing} = nothing
surfaceaxis::Union{Int,String,Nothing} = nothing
surfacecolor::Union{String,Nothing} = nothing
text::Union{Vector{String},String,Nothing} = nothing
textangle::Union{String,Nothing} = nothing
textfont::Union{Font,Nothing} = nothing
textinfo::Union{String,Nothing} = nothing
textposition::Union{String,Nothing} = nothing
texttemplate::Union{Vector{String},String,Nothing} = nothing
tickwidth::Union{Float64,Nothing} = nothing
totals::Union{Dict,Nothing} = nothing
transpose::Union{Bool,Nothing} = nothing
u::Union{Vector,Nothing} = nothing
uirevision::Union{Float64,Int,String,Nothing} = nothing
unselected::Union{Dict,Nothing} = nothing
upperfence::Union{Vector,Nothing} = nothing
v::Union{Vector,Nothing} = nothing
values::Union{Vector,Nothing} = nothing
vertexcolor::Union{Vector,Nothing} = nothing
visible::Union{String,Bool,Nothing} = nothing
w::Union{Vector,Nothing} = nothing
whiskerwidth::Union{Float64,Nothing} = nothing
width::Union{Int,Vector{Int},Nothing} = nothing
# x::Union{Vector,Matrix,Nothing} = nothing
x::Union{Vector,Nothing} = nothing
x_start::Union{Vector,Nothing} = nothing
x_end::Union{Vector,Nothing} = nothing
x0::Union{Int,String,Nothing} = nothing
xaxis::Union{String,Nothing} = nothing
xbingroup::Union{String,Nothing} = nothing
xbins::Union{Dict,Nothing} = nothing
xcalendar::Union{String,Nothing} = nothing
xgap::Union{Int,Nothing} = nothing
xperiod::Union{Float64,Int,String,Nothing} = nothing
xperiodalignment::Union{String,Nothing} = nothing
xperiod0::Union{Float64,Int,String,Nothing} = nothing
xtype::Union{String,Nothing} = nothing
# y::Union{Vector,Matrix,Nothing} = nothing
y::Union{Vector,Nothing} = nothing
y0::Union{Int,String,Nothing} = nothing
yaxis::Union{String,Nothing} = nothing
ybingroup::Union{String,Nothing} = nothing
ybins::Union{Dict,Nothing} = nothing
ycalendar::Union{String,Nothing} = nothing
ygap::Union{Int,Nothing} = nothing
yperiod::Union{Float64,Int,String,Nothing} = nothing
yperiodalignment::Union{String,Nothing} = nothing
yperiod0::Union{Float64,Int,String,Nothing} = nothing
ytype::Union{String,Nothing} = nothing
# z::Union{Vector,Matrix,Nothing} = nothing
z::Union{Vector,Nothing} = nothing
zauto::Union{Bool,Nothing} = nothing
zcalendar::Union{String,Nothing} = nothing
zhoverformat::Union{String,Nothing} = nothing
zmax::Union{Int,Nothing} = nothing
zmid::Union{Int,Nothing} = nothing
zmin::Union{Int,Nothing} = nothing
zsmooth::Union{String,Nothing} = nothing
end
const CONFIG_MAPPINGS = Dict(
:scrollzoom => :scrollZoom,
:staticplot => :staticPlot,
:displaymodebar => :displayModeBar,
:showlink => :showLink,
)
const CONFIG_DEFAULTS = Dict{Symbol, Any}(
:scrollZoom => false,
:staticPlot => false,
:showLink => false,
:editable => false,
:responsive => true,
:displayModeBar => true,
:modeBarButtonsToRemove => String[],
:modeBarButtonsToAdd => String[],
:toImageButtonOptions => Dict(
:format => "png",
:filename => "newplot",
:height => 500,
:width => 700,
:scale => 1,
)
)
const PARSER_MAPPINGS = Dict(
:type => :plot
)
const Trace = PlotData
function plotdata(data::DataFrames.DataFrame, xfeature::Symbol, yfeature::Symbol; groupfeature::Symbol, text::Union{Vector{String}, Nothing} = nothing,
mode = "markers", plottype = StipplePlotly.Charts.PLOT_TYPE_SCATTER, kwargs...) :: Vector{PlotData}
plot_collection = Vector{PlotData}()
for gf in Array(data[:, groupfeature]) |> unique!
x_feature_collection, y_feature_collection = Vector{Float64}(), Vector{Float64}()
text_collection = Vector{String}()
group_indices = data[!, groupfeature] .== gf
grouptext = text isa Vector{String} ? text[group_indices] : nothing
for (index,r) in enumerate(eachrow(data[group_indices, :]))
push!(x_feature_collection, (r[xfeature]))
push!(y_feature_collection, (r[yfeature]))
text isa Vector{String} ? push!(text_collection, (grouptext[index])) : nothing
end
plot = PlotData(;
x = x_feature_collection,
y = y_feature_collection,
mode = mode,
name = string(gf),
plot = plottype,
text = isnothing(text) ? text : text_collection,
kwargs...)
push!(plot_collection, plot)
end
plot_collection
end
function Base.show(io::IO, pd::PlotData)
output = "$(pd.plot): \n"
for f in fieldnames(typeof(pd))
prop = getproperty(pd, f)
if prop !== nothing
output *= "$f = $prop \n"
end
end
print(io, output)
end
function Base.Dict(pd::PlotData)
trace = Dict{Symbol,Any}(
:type => pd.plot
)
if pd.textfont !== nothing
trace[:textfont] = Dict(
:family => pd.textfont.family,
:size => pd.textfont.size,
:color => pd.textfont.color
)
end
if pd.insidetextfont !== nothing
trace[:insidetextfont] = Dict(
:family => pd.insidetextfont.family,
:size => pd.insidetextfont.size,
:color => pd.insidetextfont.color
)
end
if pd.outsidetextfont !== nothing
trace[:outsidetextfont] = Dict(
:family => pd.outsidetextfont.family,
:size => pd.outsidetextfont.size,
:color => pd.outsidetextfont.color
)
end
(pd.line !== nothing) && (trace[:line] = Dict(pd.line))
(pd.marker !== nothing) && (trace[:marker] = Dict(pd.marker))
(pd.error_x !== nothing) && (trace[:error_x] = Dict(pd.error_x))
(pd.error_y !== nothing) && (trace[:error_y] = Dict(pd.error_y))
(pd.error_z !== nothing) && (trace[:error_z] = Dict(pd.error_z))
(pd.colorbar !== nothing) && (trace[:colorbar] = Dict(pd.colorbar))
optionals!(trace, pd, [:align, :alignmentgroup, :alphahull, :anchor, :aspectratio, :autobinx, :autobiny,
:autocolorscale, :autocontour, :automargin,
:bandwidth, :base, :baseratio, :bingroup, :box, :boxmean, :boxpoints,
:cauto, :cells, :cliponaxis, :close, :color, :cmax, :cmid, :cmin,
:coloraxis, :colorscale, :columnorder, :columnwidth,
:connectgaps, :connector, :constraintext, :contour, :contours, :cumulative, :customdata,
:decreasing, :delta, :delaunayaxis, :direction, :dlabel, :domain, :dx, :dy,
:facecolor, :fill, :fillcolor, :flatshading,
:gauge, :groupnorm,
:header, :hidesurface, :high, :histfunc, :histnorm,
:hole, :hovertext, :hoverinfo, :hovertemplate, :hoverlabel, :hoveron, :hoverongaps,
:i, :intensity, :intensitymode, :ids, :increasing, :insidetextanchor, :insidetextorientation, :isomax, :isomin,
:j, :jitter, :k,
:labels, :label0, :legendgroup, :lighting, :lightposition, :low, :lowerfence,
:maxdisplayed, :meanline, :measure, :median, :meta,
:mode,
:name, :nbinsx, :nbinsy, :ncontours, :notched, :notchwidth, :notchspan, :number,
:offset, :offsetgroup, :opacity, :opacityscale, :colormodel, :open, :orientation,
:points, :pointpos, :projection, :pull,
:q1, :q3, :quartilemethod,
:reversescale, :rotation,
:scalegroup, :scalemode, :scene, :sd,
:selected, :selectedpoints, :showlegend,
:showscale, :side, :sizemode, :sizeref, :slices, :sort, :source, :spaceframe, :span, :spanmode,
:stackgaps, :stackgroup, :starts, :surface, :surfaceaxis, :surfacecolor,
:text, :textangle, :textinfo,
:textposition, :texttemplate, :tickwidth, :totals, :transpose,
:uirevision, :upperfence, :unselected,
:values, :vertexcolor, :visible,
:whiskerwidth, :width,
:x, :x_start, :x_end, :x0, :xaxis, :xbingroup, :xbins, :xcalendar, :xgap, :xperiod, :xperiodalignment, :xperiod0, :xtype,
:y, :y0, :yaxis, :ybingroup, :ybins, :ycalendar, :ygap, :yperiod, :yperiodalignment, :yperiod0, :ytype,
:z, :zauto, :zcalendar, :zhoverformat, :zmax, :zmid, :zmin, :zsmooth,
:geojson, :lat, :locations, :lon, :locationmode])
end
function Stipple.render(pd::PlotData, fieldname::Union{Symbol,Nothing} = nothing)
[Dict(pd)]
end
function Stipple.render(pdv::Vector{PlotData}, fieldname::Union{Symbol,Nothing} = nothing)
[Dict(pd) for pd in pdv]
end
function Stipple.render(pdvv::Vector{Vector{PlotData}}, fieldname::Union{Symbol,Nothing} = nothing)
[[Dict(pd) for pd in pdv] for pdv in pdvv]
end
# =============
# Reference: https://github.com/plotly/plotly.js/blob/master/src/plot_api/plot_config.js?package=plotly&version=3.6.0
Base.@kwdef mutable struct PlotConfig
responsive::Union{Bool,Nothing} = nothing # default: false
editable::Union{Bool,Nothing} = nothing # default: false
scrollzoom::Union{Bool,String,Nothing} = nothing # ['cartesian', 'gl3d', 'geo', 'mapbox'], [true, false]; default: gl3d+geo+mapbox'
staticplot::Union{Bool,Nothing} = nothing # default: false
displaymodebar::Union{Bool,String,Nothing} = nothing # ['hover', true, false], default: "hover"
displaylogo::Union{Bool,Nothing} = false # default: true
toimage_format::Union{String,Nothing} = nothing # one of ["png", "svg", "jpeg", "webp"]
toimage_filename::Union{String,Nothing} = nothing # "newplot"
toimage_height::Union{Int,Nothing} = nothing # 500
toimage_width::Union{Int,Nothing} = nothing # 700
toimage_scale::Union{Int,Float64,Nothing} = nothing # 1
end
function Base.show(io::IO, pc::PlotConfig)
output = "configuration: \n"
for f in fieldnames(typeof(pc))
prop = getproperty(pc, f)
if prop !== nothing
output *= "$f = $prop \n"
end
end
print(io, output)
end
function Base.Dict(pc::PlotConfig)
trace = Dict{Symbol, Any}()
if (pc.toimage_format in ["png", "svg", "jpeg", "webp"])
d = Dict{Symbol, Any}(:format => pc.toimage_format)
d[:filename] = (pc.toimage_filename === nothing) ? "newplot" : pc.toimage_filename
d[:height] = (pc.toimage_height === nothing) ? 500 : pc.toimage_height
d[:width] = (pc.toimage_width === nothing) ? 700 : pc.toimage_width
d[:scale] = (pc.toimage_scale === nothing) ? 1 : pc.toimage_scale
trace[:toImageButtonOptions] = d
end
optionals!(trace, pc, [:responsive, :editable, :scrollzoom, :staticplot, :displaymodebar, :displaylogo])
Dict{Symbol, Any}(replace(collect(keys(trace)), CONFIG_MAPPINGS...) .=> values(trace))
end
function Stipple.render(pc::PlotConfig, fieldname::Union{Symbol,Nothing} = nothing)
Dict(pc)
end
# =============
function jsonrender(x)
replace(json(render(x)), "'" => raw"\'", '"' => ''')
end
"""
plot(data::Union{Symbol,AbstractString}, args...;
layout::Union{Symbol,AbstractString,LayoutType} = Charts.PlotLayout(),
config::Union{Symbol,AbstractString,Nothing,ConfigType} = nothing, configtype = Charts.PlotConfig,
syncevents::Bool = false, syncprefix = "", class = "", keepselection::Bool = false, kwargs...) :: String where {LayoutType, ConfigType}
Generate a plotly plot with the given data and arguments.
Parameters:
- `data::Union{Symbol,AbstractString}`: name of the field that holds the plot data
- `layout::Union{Symbol,AbstractString,LayoutType}`: The layout of the plot. Default: `Charts.PlotLayout()`
- `config::Union{Symbol,AbstractString,Nothing,ConfigType}`: The configuration of the plot. Default: `nothing`
- `configtype::ConfigType`: The type of the configuration. Default: `Charts.PlotConfig`
- `syncevents::Bool`: Whether to sync events. Default: `false`
- `syncprefix::String`: Syncing is controlled via the class attribute of the plot. If left empty, the class is derived from the data name.
- `class::String`: additional class attribute for the plot
- `args`: further custom arguments
- `kwargs`: further custom keyword arguments
Forwarding plotly events is achieved by setting `syncevents` to `true` or by providing a `syncprefix`.
Model fields that the events are forwarded to are derived from the `syncprefix` and the event type, e.g. `syncprefix = "myplot"` will forward the `plotly_selected` event to the `myplot_selected` model field.
The most common event types are `plotly_selected`, `plotly_hover`, `plotly_click`, and `plotly_relayout`, which can be included in the model via `@mixin myplot::PBPlotWithEvents`.
An example of event forwarding can be found in the docstring of StipplePlotly.
"""
function plot(data::Union{Symbol,AbstractString}, args...;
layout::Union{Symbol,AbstractString,LayoutType} = Charts.PlotLayout(),
config::Union{Symbol,AbstractString,Nothing,ConfigType} = nothing, configtype = Charts.PlotConfig,
keepselection::Bool = false,
syncevents::Bool = false, syncprefix = "", class = "", kwargs...) :: String where {LayoutType, ConfigType}
plotlayout = if layout isa AbstractString
Symbol(layout)
elseif layout isa Symbol
layout
else
Symbol(jsonrender(layout))
end
plotconfig = if config isa AbstractString
Symbol(config)
elseif config isa Symbol
config
else
# clean dict and default displaylogo to false
plotconfig = render(isnothing(config) ? configtype() : config)
if plotconfig isa AbstractDict
filter!(x -> x[2] ∉ (:null, nothing), plotconfig)
plotconfig = LittleDict{Symbol, Any}(replace(keys(plotconfig), CONFIG_MAPPINGS...) .=> values(plotconfig))
haskey(plotconfig, :displaylogo) || push!(plotconfig, :displaylogo => false)
plotconfig = js_attr(plotconfig)
elseif hasproperty(plotconfig, :displaylogo) && plotconfig.displaylogo === nothing
plotconfig.displaylogo = false
end
plotconfig
end
if syncevents || ! isempty(syncprefix)
if isempty(syncprefix)
datastr = String(data)
syncprefix = endswith(datastr, "data") && length(datastr) > 4 ? datastr[1:end-4] : datastr
syncprefix = join(split(syncprefix, ['_', '.'])[1:end-1], '_')
end
class = isempty(class) ? "sync_$syncprefix" : "sync_$syncprefix $class"
end
sync = Pair{Symbol, String}[]
isempty(class) || push!(sync, :class => class)
plotly("", args...; Stipple.attributes([:layout => plotlayout, :data => Symbol(data), :config => plotconfig, :keepselection => keepselection, kwargs..., sync...])...)
end
Base.print(io::IO, a::Union{PlotLayout, PlotConfig}) = print(io, Stipple.json(a))
# =============
const PlotlyEvent = Dict{String, Any}
Base.@kwdef struct PlotlyEvents
_selected::R{PlotlyEvent} = PlotlyEvent()
_hover::R{PlotlyEvent} = PlotlyEvent()
_click::R{PlotlyEvent} = PlotlyEvent()
_relayout::R{PlotlyEvent} = PlotlyEvent()
end
Base.@kwdef struct PlotWithEvents
_data::R{Vector{PlotData}} = PlotData[]
_layout::R{PlotLayout} = PlotLayout()
_selected::R{PlotlyEvent} = PlotlyEvent()
_hover::R{PlotlyEvent} = PlotlyEvent()
_click::R{PlotlyEvent} = PlotlyEvent()
_relayout::R{PlotlyEvent} = PlotlyEvent()
end
Base.@kwdef struct PlotWithEventsReadOnly
_data::R{Vector{PlotData}} = PlotData[], READONLY
_layout::R{PlotLayout} = PlotLayout()
_selected::R{PlotlyEvent} = PlotlyEvent()
_hover::R{PlotlyEvent} = PlotlyEvent()
_click::R{PlotlyEvent} = PlotlyEvent()
_relayout::R{PlotlyEvent} = PlotlyEvent()
end
# #===#
# Parsers
function stipple_parse(::Type{PlotData}, d::Dict{String, Any})
sd = symbol_dict(d)
haskey(sd, :text) && (sd[:text] isa String || (sd[:text] = Vector{String}(sd[:text])))
haskey(sd, :selectedpoints) && (sd[:selectedpoints] = [sd[:selectedpoints]...])
sd = Dict{Symbol, Any}(replace(collect(keys(sd)), PARSER_MAPPINGS...) .=> values(sd))
# PlotData(;sd...)
typify(PlotData, sd)
end
function stipple_parse(::Type{Vector{<:PlotData}}, dd::Vector)
PlotData[stipple_parse(PlotData, d) for d in dd]
end
function stipple_parse(::Type{T}, d::Dict{Symbol, Any}) where T <: Union{Font, PlotLayout, PlotLayoutAxis, PlotLayoutGeo, PlotLayoutGrid, PlotLayoutLegend, PlotLayoutMapbox, PlotLayoutTitle}
typify(T, d)
end
function stipple_parse(::Type{T}, d::Dict{String, Any}) where T <: Union{Font, PlotLayoutAxis, PlotLayoutGeo, PlotLayoutGrid, PlotLayoutLegend, PlotLayoutMapbox, PlotLayoutTitle}
stipple_parse(T, symbol_dict(d))
end
function stipple_parse(::Type{PlotLayout}, d::Dict{String, Any})
d = symbol_dict(d)
haskey(d, :title) && (d[:title] = d[:title] isa String ? PlotLayoutTitle(; text = d[a][:title]) : PlotLayoutTitle(; d[a][:title]...))
haskey(d, :xaxis) && (d[:xaxis] = [stipple_parse(PlotLayoutAxis, d[:xaxis])])
kk = collect(keys(d))
axes = kk[startswith.(string.(kk), r"xaxis\d")]
for a in axes
push!(get!(Dict{Symbol, Any}, d, :xaxis), PlotLayoutAxis(; d[a]...))
delete!(d, a)
end
axes = kk[startswith.(string.(kk), r"yaxis\d")]
for a in axes
push!(get!(Dict{Symbol, Any}, d, :xaxis), PlotLayoutAxis(; d[a]...))
end
stipple_parse(PlotLayout, d)
end
# enhance precompilation
#=
pl = PlotLayout(
xaxis = [
PlotLayoutAxis(index = 1, title = "1"),
PlotLayoutAxis(xy = "x", index = 2, title = "2")
],
margin_r = 10,
margin_t = 20
)
d = JSON3.read(json(render(pl)), Dict{String, Any})
stipple_parse(PlotLayout, d)
=#
end
| StipplePlotly | https://github.com/GenieFramework/StipplePlotly.jl.git |
|
[
"MIT"
] | 0.14.3 | 9aee830051af43009b3c97651f124246fdabb86a | code | 90517 | module Layouts
using Genie, Stipple, StipplePlotly
import Genie.Renderer.Html: HTMLString, normal_element, register_normal_element
using Requires
const LAYOUT_TITLE_REF_CONTAINER = "container"
const LAYOUT_TITLE_REF_PAPER = "paper"
const LAYOUT_AUTO = "auto"
const LAYOUT_LEFT = "left"
const LAYOUT_CENTER = "center"
const LAYOUT_RIGHT = "right"
const LAYOUT_TOP = "top"
const LAYOUT_MIDDLE = "middle"
const LAYOUT_BOTTOM = "bottom"
const LAYOUT_ORIENTATION_VERTICAL = "v"
const LAYOUT_ORIENTATION_HORIZONTAL = "h"
const LAYOUT_ITEMSIZING_TRACE = "trace"
const LAYOUT_ITEMSIZING_CONSTANT = "constant"
const LAYOUT_CLICK_TOGGLE = "toggle"
const LAYOUT_CLICK_TOGGLEOTHERS = "toggleothers"
const LAYOUT_HIDE = "hide"
const LAYOUT_SHOW = "show"
const LAYOUT_ABOVE = "above"
const LAYOUT_BELOW = "below"
const LAYOUT_OVERLAY = "overlay"
const LAYOUT_GROUP = "group"
const LAYOUT_STACK = "stack"
function optionals!(d::Dict, ptype::Any, opts::Vector{Symbol}) :: Dict
for o in opts
if getproperty(ptype, o) !== nothing
d[o] = getproperty(ptype, o)
end
end
d
end
#===#
Base.@kwdef mutable struct Font
family::String = raw"'Open Sans', verdana, arial, sans-serif"
size::Union{Int,Float64} = 12
color::String = "#444"
end
function Font(fontsize::Union{Int,Float64})
fs = Font()
fs.size = fontsize
return fs
end
Base.:(==)(x::Font, y::Font) = x.family == y.family && x.size == y.size && x.color == y.color
Base.hash(f::Font) = hash("$(f.family)$(f.size)$(f.color)")
Base.@kwdef mutable struct Protation
lon::Union{Float64, Int64} = -234
lat::Union{Float64, Int64} = -234
roll::Union{Float64, Int64} = -234
end
function PRotation(lon::Union{Float64, Int64}, lat::Union{Float64, Int64}, roll::Union{Float64, Int64})
pr = Protation()
pr.lon = lon
pr.lat = lat
pr.roll = roll
return pr
end
"""
Mcenter()
-----------
# Properties
-----------
* `lat::Union{Float64, Int64}` - Sets the latitude of the map's center. For all projection types, the map's latitude center lies at the middle of the latitude range by default.
* `lon::Union{Float64, Int64}` - Sets the longitude of the map's center. By default, the map's longitude center lies at the middle of the longitude range for scoped projection and above `projection.rotation.lon` otherwise.
"""
Base.@kwdef mutable struct Mcenter
lon::Union{Float64, Int64} = -234
lat::Union{Float64, Int64} = -234
end
function MCenter(lon::Union{Float64, Int64}, lat::Union{Float64, Int64})
mc = Mcenter()
mc.lon = lon
mc.lat = lat
return mc
end
#===#
"""
ColorBar()
----------
# Examples
----------
```
julia>
```
-----------
# Properties
-----------
* `bgcolor::String` - Sets the color of padded area.
* `bordercolor::String` - Sets the axis line color. Default = `"#444"`
* `borderwidth::Int` - Sets the width (in px) or the border enclosing this color bar. Default = `0`
* `dtick::Union{Float64,Int,String}` - Sets the step in-between ticks on this axis. Use with `tick0`. Must be a positive number, or special strings available to "log" and "date" axes. If the axis `type` is "log", then ticks are set every 10^(n"dtick) where n is the tick number. For example, to set a tick mark at 1, 10, 100, 1000, ... set dtick to 1. To set tick marks at 1, 100, 10000, ... set dtick to 2. To set tick marks at 1, 5, 25, 125, 625, 3125, ... set dtick to log_10(5), or 0.69897000433. "log" has several special values; "L<f>", where `f` is a positive number, gives ticks linearly spaced in value (but not position). For example `tick0` = 0.1, `dtick` = "L0.5" will put ticks at 0.1, 0.6, 1.1, 1.6 etc. To show powers of 10 plus small digits between, use "D1" (all digits) or "D2" (only 2 and 5). `tick0` is ignored for "D1" and "D2". If the axis `type` is "date", then you must convert the time to milliseconds. For example, to set the interval between ticks to one day, set `dtick` to 86400000.0. "date" also has special values "M<n>" gives ticks spaced by a number of months. `n` must be a positive integer. To set ticks on the 15th of every third month, set `tick0` to "2000-01-15" and `dtick` to "M3". To set ticks every 4 years, set `dtick` to "M48"
* `exponentformat::String` - Determines a formatting rule for the tick exponents. For example, consider the number 1,000,000,000. If "none", it appears as 1,000,000,000. If "e", 1e+9. If "E", 1E+9. If "power", 1x10^9 (with 9 in a super script). If "SI", 1G. If "B", 1B. Default - `"B"`
* `len::Union{Float64,Int}` - Sets the length of the color bar This measure excludes the padding of both ends. That is, the color bar length is this length minus the padding on both ends.
* `lenmode::String` - Determines whether the length of the color bar is set in units of plot "fraction" or in "pixels". Use `len` to set the value.
* `minexponent::Int` - Hide SI prefix for 10^n if |n| is below this number. This only has an effect when `tickformat` is "SI" or "B". Default - `0`
* `nticks::Int` - Specifies the maximum number of ticks for the particular axis. The actual number of ticks will be chosen automatically to be less than or equal to `nticks`. Has an effect only if `tickmode` is set to "auto". Default - `0`
* `outlinecolor::String` - Sets the axis line color.
* `outlinewidth::Int` - Sets the width (in px) of the axis line.
* `separatethousands::Bool` - If "true", even 4-digit integers are separated
* `showexponent::Bool` - If "all", all exponents are shown besides their significands. If "first", only the exponent of the first tick is shown. If "last", only the exponent of the last tick is shown. If "none", no exponents appear.
* `showticklabels::Bool` - Determines whether or not the tick labels are drawn.
* `showtickprefix::Bool` - If "all", all tick labels are displayed with a prefix. If "first", only the first tick is displayed with a prefix. If "last", only the last tick is displayed with a suffix. If "none", tick prefixes are hidden.
* `showticksuffix::Bool` - Same as `showtickprefix` but for tick suffixes.
* `thickness::Int` - Sets the thickness of the color bar This measure excludes the size of the padding, ticks and labels.
* `thicknessmode::String` - Determines whether the thickness of the color bar is set in units of plot "fraction" or in "pixels". Use `thickness` to set the value.
* `tick0::Union{Float64,Int,String}` - Sets the placement of the first tick on this axis. Use with `dtick`. If the axis `type` is "log", then you must take the log of your starting tick (e.g. to set the starting tick to 100, set the `tick0` to 2) except when `dtick`=*L<f>* (see `dtick` for more info), where the axis starts at zero. If the axis `type` is "date", it should be a date string, like date data. If the axis `type` is "category", it should be a number, using the scale where each category is assigned a serial number from zero in the order it appears.
* `tickangle::Union{String,Int,Float64}` - Sets the angle of the tick labels with respect to the horizontal. For example, a `tickangle` of -90 draws the tick labels vertically.
* `tickcolor::String` - Sets the tick color.
* `tickformat::String` - Sets the tick label formatting rule using d3 formatting mini-languages which are very similar to those in Python. For numbers, see: https://github.com/d3/d3-format/tree/v1.4.5#d3-format. And for dates see: https://github.com/d3/d3-time-format/tree/v2.2.3#locale_format. We add two items to d3's date formatter: "%h" for half of the year as a decimal number as well as "%{n}f" for fractional seconds with n digits. For example, "2016-10-13 09:15:23.456" with tickformat "%H~%M~%S.%2f" would display "09~15~23.46"
* `tickformatstops::Dict` - Array of object where each object has one or more of the keys - "dtickrange", "value", "enabled", "name", "templateitemname"
* `ticklabeloverflow::String` - Determines how we handle tick labels that would overflow either the graph div or the domain of the axis. The default value for inside tick labels is "hide past domain". In other cases the default is "hide past div".
* `ticklabelposition::String` - Determines where tick labels are drawn relative to the ticks. Left and right options are used when `orientation` is "h", top and bottom when `orientation` is "v". Type: enumerated , one of ( "outside" | "inside" | "outside top" | "inside top" | "outside left" | "inside left" | "outside right" | "inside right" | "outside bottom" | "inside bottom" ) Default: "outside"
* `ticklabelstep::String` - Sets the spacing between tick labels as compared to the spacing between ticks. A value of 1 (default) means each tick gets a label. A value of 2 means shows every 2nd label. A larger value n means only every nth tick is labeled. `tick0` determines which labels are shown. Not implemented for axes with `type` "log" or "multicategory", or when `tickmode` is "array".
* `ticklen::Int` - Sets the tick length (in px). Type: number greater than or equal to 0 | Default: 5
* `tickmode::String` - Sets the tick mode for this axis. If "auto", the number of ticks is set via `nticks`. If "linear", the placement of the ticks is determined by a starting position `tick0` and a tick step `dtick` ("linear" is the default value if `tick0` and `dtick` are provided). If "array", the placement of the ticks is set via `tickvals` and the tick text is `ticktext`. ("array" is the default value if `tickvals` is provided). Type: enumerated , one of ( "auto" | "linear" | "array" ) Default: "array"
* `tickprefix::String` - Sets a tick label prefix. Type: string Default: ""
* `ticks::String` - Determines whether ticks are drawn or not. If "", this axis' ticks are not drawn. If "outside" ("inside"), this axis' are drawn outside (inside) the axis lines. Type: enumerated , one of ( "outside" | "inside" | "" ) Default: ""
* `ticksuffix::String` - Sets a tick label suffix. Type: string Default: ""
* `ticktext::Vector{String}` - Sets the text displayed at the ticks position via `tickvals`. Only has an effect if `tickmode` is set to "array". Used with `tickvals`. Type: vector of strings
* `tickvals::Vector{Float64}` - Sets the values at which ticks on this axis appear. Only has an effect if `tickmode` is set to "array". Type: vector of numbers
* `tickwidth::Int` - Sets the tick width (in px). Type: number greater than or equal to 0 | Default: 1
* `title_font::Font` - Sets this color bar's title font.
* `title_side::String` - Determines the location of the colorbar title with respect to the color bar. Defaults to "top" when `orientation` if "v" and defaults to "right" when `orientation` if "h".
* `title_text::String` - Sets the title of the color bar.
* `x::Float64` - Sets the x position of the color bar (in plot fraction). Defaults to 1.02 when `orientation` is "v" and 0.5 when `orientation` is "h". Type: number between or equal to -2 and 3
* `xanchor::String` - Sets this color bar's horizontal position anchor. This anchor binds the `x` position to the "left", "center" or "right" of the color bar. Defaults to "left" when `orientation` is "v" and "center" when `orientation` is "h". Type: enumerated , one of ( "auto" | "left" | "center" | "right" )
* `xpad::Int` - Sets the amount of padding (in px) along the x direction. Type: number greater than or equal to 0 | Default: 0
* `y::Float64` - Sets the y position of the color bar (in plot fraction). Defaults to 0.98 when `orientation` is "v" and 0.5 when `orientation` is "h". Type: number between or equal to -2 and 3
* `yanchor::String` - Sets this color bar's vertical position anchor This anchor binds the `y` position to the "top", "middle" or "bottom" of the color bar. Defaults to "middle" when `orientation` is "v" and "bottom" when `orientation` is "h". Type: enumerated , one of ("top" | "middle" | "bottom" )
* `ypad::Int` - Sets the amount of padding (in px) along the y direction. Type: number greater than or equal to 0 | Default: 10
"""
Base.@kwdef mutable struct ColorBar
bgcolor::Union{String,Nothing} = nothing # "rgba(0,0,0,0)"
bordercolor::Union{String,Nothing} = nothing # "#444"
borderwidth::Union{Int,Nothing} = nothing # 0
dtick::Union{Float64,Int,String,Nothing} = nothing
exponentformat::Union{String,Nothing} = nothing # none" | "e" | "E" | "power" | "SI" | "B", default is B
len::Union{Float64,Int,Nothing} = nothing # number greater than or equal to 0
lenmode::Union{String,Nothing} = nothing # "fraction" | "pixels", default is fraction | Default: "fraction"
minexponent::Union{Int,Nothing} = nothing # number greater than or equal to 0 | Default: 3
nticks::Union{Int,Nothing} = nothing # number greater than or equal to 0 | Default: 0
orientation::Union{String,Nothing} = nothing # "v" | "h", default is "v"
outlinecolor::Union{String,Nothing} = nothing # "#444"
outlinewidth::Union{Int,Nothing} = nothing # number greater than or equal to 0 | Default: 1
separatethousands::Union{Bool,Nothing} = nothing # true | false, default is false
showexponent::Union{String,Nothing} = nothing # "all" | "first" | "last" | "none", default is "all"
showticklabels::Union{Bool,Nothing} = nothing # true | false, default is true
showtickprefix::Union{String,Nothing} = nothing # "all" | "first" | "last" | "none", default is all
showticksuffix::Union{String,Nothing} = nothing # "all" | "first" | "last" | "none", default is "all"
thickness::Union{Int,Nothing} = nothing # number greater than or equal to 0 | Default: 30
thicknessmode::Union{String,Nothing} = nothing # "fraction" | "pixels", default is fraction | Default: "pixels"
tick0::Union{Float64,Int,String,Nothing} = nothing # number or categorical coordinate string
tickangle::Union{String,Int,Float64,Nothing} = nothing # Default: "auto"
tickcolor::Union{String,Nothing} = nothing # Default: "#444"
tickfont::Union{Font,Nothing} = nothing # Font Struct
tickformat::Union{String,Nothing} = nothing # string, default is ""
tickformatstops::Union{Dict,Nothing} = nothing # Dict containing properties
ticklabeloverflow::Union{String,Nothing} = nothing # "allow" | "hide past div" | "hide past domain"
ticklabelposition::Union{String,Nothing} = nothing # "outside" | "inside" | "outside top" | "inside top" | "outside bottom" | "inside bottom", default is "outside"
ticklabelstep::Union{Int,Nothing} = nothing # number greater than or equal to 1 | Default: 1
ticklen::Union{Int,Nothing} = nothing # number greater than or equal to 0 | Default: 5
tickmode::Union{String,Nothing} = nothing # "auto" | "linear" | "array", default is "array"
tickprefix::Union{String,Nothing} = nothing # string, default is ""
ticks::Union{String,Nothing} = nothing # "outside" | "inside" | "" | Default: ""
ticksuffix::Union{String,Nothing} = nothing # string, default is ""
ticktext::Union{Vector{String},Nothing} = nothing # Vector of strings
tickvals::Union{Vector{Float64},Vector{Int},Nothing} = nothing
tickwidth::Union{Int,Nothing} = nothing # number greater than or equal to 0 | Default: 1
x::Union{Float64,Nothing} = nothing # 1.02
xanchor::Union{String,Nothing} = nothing # "left" | "center" | "right", default is left
xpad::Union{Int,Nothing} = nothing # 10
yanchor::Union{String,Nothing} = nothing # "top" | "middle" | "bottom", default is middle
ypad::Union{Int,Nothing} = nothing # 10
# needs special treatment:
title_font::Union{Font,Nothing} = nothing # Font()
title_side::Union{String,Nothing} = nothing # LAYOUT_LEFT
title_text::Union{String,Nothing} = nothing # ""
end
function Base.show(io::IO, cb::ColorBar)
output = "ColorBar: \n"
for f in fieldnames(typeof(cb))
prop = getproperty(cb, f)
if prop !== nothing
output *= "$f = $prop \n"
end
end
print(io, output)
end
function Base.Dict(cb::ColorBar)
trace = Dict{Symbol, Any}()
d = Dict{Symbol, Any}()
(cb.title_text !== nothing) && (d[:text] = cb.title_text)
(cb.title_font !== nothing) && (d[:font] = cb.title_font)
(cb.title_side !== nothing) && (d[:side] = cb.title_side)
(length(d) > 0) && (trace[:title] = d)
optionals!(trace, cb, [
:bgcolor, :bordercolor, :borderwidth, :dtick, :exponentformat, :len, :lenmode, :minexponent, :nticks, :orientation,
:outlinecolor, :outlinewidth, :separatethousands, :showexponent, :showticklabels, :showtickprefix, :showticksuffix,
:thickness, :thicknessmode, :tick0, :tickangle, :tickcolor, :tickfont, :tickformat, :tickformatstops, :ticklabeloverflow,
:ticklabelposition, :ticklabelstep, :ticklen, :tickmode, :tickprefix, :ticks, :ticksuffix, :ticktext, :tickvals, :tickwidth,
:x, :xanchor, :xpad, :yanchor, :ypad
])
end
function Stipple.render(cb::ColorBar, fieldname::Union{Symbol,Nothing} = nothing)
Dict(cb)
end
function ColorBar(text, title_font_size::Union{Int,Float64}, side)
cb = ColorBar()
cb.title_text = text
cb.title_font = Font(title_font_size)
cb.title_side = side
cb
end
#===#
"""
ErrorBar()
----------
# Examples
----------
```
julia> error_x = ErrorBar(
array = [1.2, 2.6, 3.1],
type = "data"
)
```
-----------
# Properties
-----------
* `array::Vector{Float64}` - Sets the data corresponding the length of each error bar. Values are plotted relative to the underlying data.
* `arrayminus::Vector{Float64}` - Sets the data corresponding the length of each error bar in the bottom (left) direction for vertical (horizontal) bars Values are plotted relative to the underlying data.
* `color::String` - Sets the stoke color of the error bars.
* `symmetric::Bool` - Determines whether or not the error bars have the same length in both direction (top/bottom for vertical bars, left/right for horizontal bars.
* `thickness::Int` - Sets the thickness (in px) of the error bars. Type: greater than or equal to 0. Default: 2
* `traceref::Int` - Type: Integer greater than or equal to 0. Default: 0
* `tracerefminus::Int` - Type: Integer greater than or equal to 0. Default: 0
* `type::String` - Determines the rule used to generate the error bars. If "constant`, the bar lengths are of a constant value. Set this constant in `value`. If "percent", the bar lengths correspond to a percentage of underlying data. Set this percentage in `value`. If "sqrt", the bar lengths correspond to the square of the underlying data. If "data", the bar lengths are set with data set `array`. Type: enumerated , one of ( "percent" | "constant" | "sqrt" | "data" )
* `value::Float64` - Sets the value of either the percentage (if `type` is set to "percent") or the constant (if `type` is set to "constant") in the case of "constant" `type`. Type: greater than or equal to 0. Default: 10
* `valueminus::Float64` - Sets the value of either the percentage (if `type` is set to "percent") or the constant (if `type` is set to "constant") corresponding to the lengths of the error bars in the bottom (left) direction for vertical (horizontal) bars. Type: number greater than or equal to 0 | Default: 10
* `visible::Bool` - Determines whether or not this set of error bars is visible.
* `width::Int` - Sets the width (in px) of the cross-bar at both ends of the error bars. Type: greater than or equal to 0
"""
Base.@kwdef mutable struct ErrorBar
array::Union{Vector{Float64},Nothing} = nothing # Vector of numbers
arrayminus::Union{Vector{Float64},Nothing} = nothing # Vector of numbers
color::Union{String,Nothing} = nothing # Color string
copy_ystyle::Union{Bool,Nothing} = nothing # true | false
symmetric::Union{Bool,Nothing} = nothing
thickness::Union{Int,Nothing} = nothing # 2
traceref::Union{Int,Nothing} = nothing # 0
tracerefminus::Union{Int,Nothing} = nothing # 0
type::Union{String,Nothing} = nothing # "percent" | "constant" | "sqrt" | "data"
value::Union{Float64,Nothing} = nothing # 10
valueminus::Union{Float64,Nothing} = nothing # 10
visible::Union{Bool,Nothing} = nothing
width::Union{Int,Nothing} = nothing # 0
end
function Base.show(io::IO, eb::ErrorBar)
output = "Errorbar: \n"
for f in fieldnames(typeof(eb))
prop = getproperty(eb, f)
if prop !== nothing
output *= "$f = $prop \n"
end
end
print(io, output)
end
function ErrorBar(error_array::Vector; color::Union{String,Nothing} = nothing)
eb = ErrorBar(visible=true, array=error_array, type="data", symmetric=true)
(color !== nothing) && (eb.color = color)
eb
end
function ErrorBar(error_array::Vector, error_arrayminus::Vector; color::Union{String,Nothing} = nothing)
eb = ErrorBar(visible=true, array=error_array, type="data", symmetric=false, arrayminus=error_arrayminus)
(color !== nothing) && (eb.color = color)
eb
end
function ErrorBar(error_value::Number; color::Union{String,Nothing} = nothing)
eb = ErrorBar(visible=true, value=error_value, type="percent", symmetric=true)
(color !== nothing) && (eb.color = color)
eb
end
function ErrorBar(error_value::Number, error_valueminus::Number; color::Union{String,Nothing} = nothing)
eb = ErrorBar(visible=true, value=error_value, type="percent", symmetric=false, valueminus=error_valueminus)
(color !== nothing) && (eb.color = color)
eb
end
function Base.Dict(eb::ErrorBar)
trace = Dict{Symbol, Any}()
optionals!(trace, eb, [
:array, :arrayminus, :color, :copy_ystyle, :symmetric, :thickness,
:traceref, :tracerefminus, :type, :value, :valueminus, :visible, :width
])
end
function Stipple.render(eb::ErrorBar, fieldname::Union{Symbol,Nothing} = nothing)
Dict(eb)
end
#===#
"""
PlotAnnotation()
----------
# Examples
----------
```
julia>
```
-----------
# Properties
-----------
* `align::String` -Sets the horizontal alignment of the `text` within the box. Has an effect only if `text` spans two or more lines (i.e. `text` contains one or more <br> HTML tags) or if an explicit width is set to override the text width. Type: enumerated , one of ( `"left"` | `"center"` | `"right"` ) | Default: `"center"`
* `arrowcolor::String` -Sets the color of the annotation arrow.
* `arrowhead::Int` - Sets the end annotation arrow head style. Type: integer between or equal to `0` and `8` | Default: `1`
* `arrowside::String` - Sets the annotation arrow head position. Type: flaglist string. Any combination of `"end"`, `"start"` joined with a `"+"` OR `"none"` | Default: `"end"`
* `arrowsize::Float64` - Sets the size of the end annotation arrow head, relative to `arrowwidth`. A value of 1 (default) gives a head about 3x as wide as the line. Type: number greater than or equal to `0.3` | Default: `1`
* `arrowwidth::Float64` - Sets the width (in px) of annotation arrow line. Type: number greater than or equal to `0.1`
* `ax::Union{String,Int,Float64}` - Sets the x component of the arrow tail about the arrow head. If `axref` is `pixel`, a positive (negative) component corresponds to an arrow pointing from right to left (left to right). If `axref` is not `pixel` and is exactly the same as `xref`, this is an absolute value on that axis, like `x`, specified in the same coordinates as `xref`. Type: number or categorical coordinate string
* `axref::String` - Indicates in what coordinates the tail of the annotation (ax,ay) is specified. If set to a ax axis id (e.g. "ax" or "ax2"), the `ax` position refers to a ax coordinate. If set to "paper", the `ax` position refers to the distance from the left of the plotting area in normalized coordinates where "0" ("1") corresponds to the left (right). If set to a ax axis ID followed by "domain" (separated by a space), the position behaves like for "paper", but refers to the distance in fractions of the domain length from the left of the domain of that axis: e.g., "ax2 domain" refers to the domain of the second ax axis and a ax position of 0.5 refers to the point between the left and the right of the domain of the second ax axis. In order for absolute positioning of the arrow to work, "axref" must be exactly the same as "xref", otherwise "axref" will revert to "pixel" (explained next). For relative positioning, "axref" can be set to "pixel", in which case the "ax" value is specified in pixels relative to "x". Absolute positioning is useful for trendline annotations which should continue to indicate the correct trend when zoomed. Relative positioning is useful for specifying the text offset for an annotated point. Type: enumerated , one of ( `"pixel"` | `"/^x([2-9]|[1-9][0-9]+)?( domain)?\$/"`) | Default: `"pixel"`
* `ay::Union{String,Int,Float64}` - Sets the y component of the arrow tail about the arrow head. If `ayref` is `pixel`, a positive (negative) component corresponds to an arrow pointing from bottom to top (top to bottom). If `ayref` is not `pixel` and is exactly the same as `yref`, this is an absolute value on that axis, like `y`, specified in the same coordinates as `yref`. Type: number or categorical coordinate string
* `ayref::String` - Indicates in what coordinates the tail of the annotation (ax,ay) is specified. If set to a ay axis id (e.g. "ay" or "ay2"), the `ay` position refers to a ay coordinate. If set to "paper", the `ay` position refers to the distance from the bottom of the plotting area in normalized coordinates where "0" ("1") corresponds to the bottom (top). If set to a ay axis ID followed by "domain" (separated by a space), the position behaves like for "paper", but refers to the distance in fractions of the domain length from the bottom of the domain of that axis: e.g., "ay2 domain" refers to the domain of the second ay axis and a ay position of 0.5 refers to the point between the bottom and the top of the domain of the second ay axis. In order for absolute positioning of the arrow to work, "ayref" must be exactly the same as "yref", otherwise "ayref" will revert to "pixel" (explained next). For relative positioning, "ayref" can be set to "pixel", in which case the "ay" value is specified in pixels relative to "y". Absolute positioning is useful for trendline annotations which should continue to indicate the correct trend when zoomed. Relative positioning is useful for specifying the text offset for an annotated point. Type: enumerated , one of ( `"pixel"` | `"/^x([2-9]|[1-9][0-9]+)?( domain)?\$/"`) | Default: `"pixel"`
* `bgcolor::String` -Sets the background color of the annotation. Default: `"rgba(0,0,0,0)"`
* `bordercolor::String` - Sets the color of the border enclosing the annotation `text`. Default: `"rgba(0,0,0,0)"`
* `borderpad::Int` - Sets the padding (in px) between the `text` and the enclosing border. Default: `1`
* `borderwidth::Int` - Sets the width (in px) of the border enclosing the annotation `text`. Type: number greater than or equal to 0 | Default: `1`
* `captureevents::Bool` - Determines whether the annotation text box captures mouse move and click events, or allows those events to pass through to data points in the plot that may be behind the annotation. By default `captureevents` is "false" unless `hovertext` is provided. If you use the event `plotly_clickannotation` without `hovertext` you must explicitly enable `captureevents`.
* `font::Font` - Sets the annotation text font.
* `height::Int` - Sets an explicit height for the text box. null (default) lets the text set the box height. Taller text will be clipped. Type: number greater than or equal to `1`
* `hoverlabel::Dict` - object containing one or more of the keys listed: `bgcolor` `bordercolor` `font`
* `name::String` - When used in a template, named items are created in the output figure in addition to any items the figure already has in this array. You can modify these items in the output figure by making your own item with `templateitemname` matching this `name` alongside your modifications (including `visible: false` or `enabled: false` to hide it). Has no effect outside of a template.
* `opacity::Float64` - Sets the opacity of the annotation (text + arrow). Type: number between or equal to `0` and `1` | Default: `1`
* `showarrow::Bool` - Determines whether or not the annotation is drawn with an arrow. If "true", `text` is placed near the arrow's tail. If "false", `text` lines up with the `x` and `y` provided. Default: `true`
* `standoff::Int` - Sets a distance, in pixels, to move the end arrowhead away from the position it is pointing at, for example to point at the edge of a marker independent of zoom. Note that this shortens the arrow from the `ax` / `ay` vector, in contrast to `xshift` / `yshift` which moves everything by this amount. Type: number greater than or equal to `0` | Default: `0`
* `startarrowhead::Int` - Sets the start annotation arrow head style. Type: integer between or equal to `0` and `8` | Default: `1`
* `startarrowsize::Int` - Sets the size of the start annotation arrow head, relative to `arrowwidth`. A value of 1 (default) gives a head about 3x as wide as the line. Type: number greater than or equal to `0.3` | Default: `1`
* `startstandoff::Int` - Sets a distance, in pixels, to move the start arrowhead away from the position it is pointing at, for example to point at the edge of a marker independent of zoom. Note that this shortens the arrow from the `ax` / `ay` vector, in contrast to `xshift` / `yshift` which moves everything by this amount. Type: number greater than or equal to `0` | Default: `0`
* `templateitemname::String` - Used to refer to a named item in this array in the template. Named items from the template will be created even without a matching item in the input figure, but you can modify one by making an item with `templateitemname` matching its `name`, alongside your modifications (including `visible: false` or `enabled: false` to hide it). If there is no template or no matching item, this item will be hidden unless you explicitly show it with `visible: true`.
* `text::String` - Sets the text associated with the annotation. Plotly uses a subset of HTML tags to do things like newline (<br>), bold (<b></b>), italics (<i></i>), hyperlinks (<a href='...'></a>). Tags <em>, <sup>, <sub> <span> are also supported. Type: string
* `textangle::Union{Int,Float64}` - Sets the angle at which the `text` is drawn with respect to the horizontal. Type: `angle` | Default: `0`
* `valign::String` - Sets the vertical alignment of the `text` within the box. Has an effect only if an explicit height is set to override the text height. Type: enumerated , one of ( `"top"` | `"middle"` | `"bottom"`) | Default: `"middle"`
* `visible::Bool` `visible` - Determines whether or not this annotation is visible. Type: boolean | Default: `true`
* `width::Int` - Sets an explicit width for the text box. null (default) lets the text set the box width. Wider text will be clipped. Type: number greater than or equal to `1`
* `x::Union{String,Int,Float64}` - Sets the annotation's x position. If the axis `type` is "log", then you must take the log of your desired range. If the axis `type` is "date", it should be date strings, like date data, though Date objects and unix milliseconds will be accepted and converted to strings. If the axis `type` is "category", it should be numbers, using the scale where each category is assigned a serial number from zero in the order it appears.
* `xanchor::String` - Sets the text box's horizontal position anchor This anchor binds the `x` position to the "left", "center" or "right" of the annotation. For example, if `x` is set to 1, `xref` to "paper" and `xanchor` to "right" then the right-most portion of the annotation lines up with the right-most edge of the plotting area. If "auto", the anchor is equivalent to "center" for data-referenced annotations or if there is an arrow, whereas for paper-referenced with no arrow, the anchor picked corresponds to the closest side. Type: enumerated , one of ( `"auto"` | `"left"` | `"center"` | `"right"`) | Default: `"auto"`
* `xref::Union{String,Int,Float64}` - Sets the annotation's x coordinate axis. If set to a x axis id (e.g. "x" or "x2"), the `x` position refers to a x coordinate. If set to "paper", the `x` position refers to the distance from the left of the plotting area in normalized coordinates where "0" ("1") corresponds to the left (right). If set to a x axis ID followed by "domain" (separated by a space), the position behaves like for "paper", but refers to the distance in fractions of the domain length from the left of the domain of that axis: e.g., "x2 domain" refers to the domain of the second x axis and a x position of 0.5 refers to the point between the left and the right of the domain of the second x axis. Type: enumerated , one of ( `"paper"` | `"/^x([2-9]|[1-9][0-9]+)?( domain)?\$/"` )
* `xshift::Union{Int,Float64}` - Shifts the position of the whole annotation and arrow to the right (positive) or left (negative) by this many pixels. Default: `0`
* `y::Union{String,Int,Float64}` - Sets the annotation's y position. If the axis `type` is "log", then you must take the log of your desired range. If the axis `type` is "date", it should be date strings, like date data, though Date objects and unix milliseconds will be accepted and converted to strings. If the axis `type` is "category", it should be numbers, using the scale where each category is assigned a serial number from zero in the order it appears.
* `yanchor::Union{String}` - Sets the text box's vertical position anchor This anchor binds the `y` position to the "top", "middle" or "bottom" of the annotation. For example, if `y` is set to 1, `yref` to "paper" and `yanchor` to "top" then the top-most portion of the annotation lines up with the top-most edge of the plotting area. If "auto", the anchor is equivalent to "middle" for data-referenced annotations or if there is an arrow, whereas for paper-referenced with no arrow, the anchor picked corresponds to the closest side. Type: enumerated , one of ( `"auto"` | `"top"` | `"middle"` | `"bottom"`) | Default: `"auto"`
* `yref::Union{String,Int,Float64}` - Sets the annotation's y coordinate axis. If set to a y axis id (e.g. "y" or "y2"), the `y` position refers to a y coordinate. If set to "paper", the `y` position refers to the distance from the bottom of the plotting area in normalized coordinates where "0" ("1") corresponds to the bottom (top). If set to a y axis ID followed by "domain" (separated by a space), the position behaves like for "paper", but refers to the distance in fractions of the domain length from the bottom of the domain of that axis: e.g., "y2 domain" refers to the domain of the second y axis and a y position of 0.5 refers to the point between the bottom and the top of the domain of the second y axis. Type: enumerated , one of ( `"paper"` | `"/^x([2-9]|[1-9][0-9]+)?( domain)?\$/"` )
* `yshift::Union{Int,Float64}` - Shifts the position of the whole annotation and arrow up (positive) or down (negative) by this many pixels. Default: `0`
"""
Base.@kwdef mutable struct PlotAnnotation
align::Union{String,Nothing} = nothing
arrowcolor::Union{String,Nothing} = nothing
arrowhead::Union{Int,Nothing} = nothing
arrowside::Union{String,Nothing} = nothing
arrowsize::Union{Float64,Nothing} = nothing
arrowwidth::Union{Float64,Nothing} = nothing
ax::Union{String,Int,Float64,Nothing} = nothing
axref::Union{String,Nothing} = nothing
ay::Union{String,Int,Float64,Nothing} = nothing
ayref::Union{String,Nothing} = nothing
bgcolor::Union{String,Nothing} = nothing
bordercolor::Union{String,Nothing} = nothing
borderpad::Union{Int,Nothing} = nothing
borderwidth::Union{Int,Nothing} = nothing
captureevents::Union{Bool,Nothing} = nothing
# TODO: clicktoshow
# TODO: xclick
# TODO: yclick
font::Union{Font,Nothing} = nothing
height::Union{Float64,Int,Nothing} = nothing
hoverlabel::Union{Dict,Nothing} = nothing
name::Union{String,Nothing} = nothing
opacity::Union{Float64,Nothing} = nothing
showarrow::Union{Bool,Nothing} = nothing
standoff::Union{Int,Nothing} = nothing
startarrowhead::Union{Int,Nothing} = nothing
startarrowsize::Union{Float64,Nothing} = nothing
startstandoff::Union{Int,Nothing} = nothing
templateitemname::Union{String,Nothing} = nothing
text::Union{String,Nothing} = nothing
textangle::Union{Float64,Int,Nothing} = nothing
valign::Union{String,Nothing} = nothing
visible::Union{Bool,Nothing} = nothing
width::Union{Float64,Int,Nothing} = nothing
x::Union{String,Int,Float64,Nothing} = nothing
xanchor::Union{String,Nothing} = nothing
xref::Union{String,Int,Float64,Nothing} = nothing
xshift::Union{Int,Float64,Nothing} = nothing
y::Union{String,Int,Float64,Nothing} = nothing
yanchor::Union{String,Nothing} = nothing
yref::Union{String,Int,Float64,Nothing} = nothing
yshift::Union{Int,Float64,Nothing} = nothing
end
function Base.show(io::IO, an::PlotAnnotation)
output = "Annotation: \n"
for f in fieldnames(typeof(an))
prop = getproperty(an, f)
if prop !== nothing
output *= "$f = $prop \n"
end
end
print(io, output)
end
function Base.Dict(an::PlotAnnotation)
trace = Dict{Symbol,Any}()
if an.font !== nothing
trace[:font] = Dict(
:family => an.font.family,
:size => an.font.size,
:color => an.font.color
)
end
if an.hoverlabel !== nothing
trace[:hoverlabel] = an.hoverlabel
end
optionals!(trace, an, [:align, :arrowcolor, :arrowhead, :arrowside, :arrowsize, :arrowwidth,
:ax, :axref, :ay, :ayref, :bgcolor, :bordercolor, :borderpad, :borderwidth, :captureevents,
:height, :hoverlabel, :name, :opacity, :showarrow, :standoff, :startarrowhead, :startarrowsize,
:startstandoff, :templateitemname, :text, :textangle, :valign, :visible, :width, :x, :xanchor,
:xref, :xshift, :y, :yanchor, :yref, :yshift])
end
function Stipple.render(anv::Vector{PlotAnnotation}, fieldname::Union{Symbol,Nothing} = nothing)
[Dict(an) for an in anv]
end
#===#
"""
PlotAnnotation()
----------
# Examples
----------
```
julia>
```
-----------
# Properties
-----------
* `anchor::String` - If set to an opposite-letter axis id (e.g. `x2`, `y`), this axis is bound to the corresponding opposite-letter axis. If set to "free", this axis' position is determined by `position`. Type: enumerated , one of ( `"free"` | `"/^x([2-9]|[1-9][0-9]+)?( domain)?\$/"` |` "/^y([2-9]|[1-9][0-9]+)?( domain)?\$/"` )
* `automargin::Bool` - Determines whether this axis' margin is computed automatically. Type: boolean
* `autorange::Bool` - Determines whether or not the range of this axis is computed in relation to the input data. See `rangemode` for more info. If `range` is provided, then `autorange` is set to "false". Type: enumerated , one of ( `true` | `false` | `"reversed"` ) | Default: `true`
* `autotypenumbers::String` - Using "strict" a numeric string in trace data is not converted to a number. Using "convert types" a numeric string in trace data may be treated as a number during automatic axis `type` detection. Defaults to layout.autotypenumbers. Type: enumerated , one of ( `"strict"` | `"convert types"` ) | Default: `"convert types"`
* `calendar::String` - Sets the calendar system to use for `range` and `tick0` if this is a date axis. This does not set the calendar for interpreting data on this axis, that's specified in the trace or via the global `layout.calendar`. Type: enumerated , one of ( `"gregorian"` | `"chinese"` | `"coptic"` | `"discworld"` | `"ethiopian"` | `"hebrew"` | `"islamic"` | `"julian"` | `"mayan"` | `"nanakshahi"` | `"nepali"` | `"persian"` | `"jalali"` | `"taiwan"` | `"thai"` | `"ummalqura"` ) | Default: `"gregorian"`
* `categoryarray::Vector{Float64}` - Sets the order in which categories on this axis appear. Only has an effect if `categoryorder` is set to "array". Used with `categoryorder`. Type: Vector
* `categoryorder::String` - Specifies the ordering logic for the case of categorical variables. By default, plotly uses "trace", which specifies the order that is present in the data supplied. Set `categoryorder` to "category ascending" or "category descending" if order should be determined by the alphanumerical order of the category names. Set `categoryorder` to "array" to derive the ordering from the attribute `categoryarray`. If a category is not found in the `categoryarray` array, the sorting behavior for that attribute will be identical to the "trace" mode. The unspecified categories will follow the categories in `categoryarray`. Set `categoryorder` to "total ascending" or "total descending" if order should be determined by the numerical order of the values. Similarly, the order can be determined by the min, max, sum, mean or median of all the values. Type: enumerated , one of ( `"trace"` | `"category ascending"` | `"category descending"` | `"array"` | `"total ascending"` | `"total descending"` ) | Default: `"trace"`
* `constrain::String` - If this axis needs to be compressed (either due to its own `scaleanchor` and `scaleratio` or those of the other axis), determines how that happens: by increasing the "range", or by decreasing the "domain". Default is "domain" for axes containing image traces, "range" otherwise. Type: enumerated , one of ( `"domain"` | `"range"` )
* `constraintoward::String` - If this axis needs to be compressed (either due to its own `scaleanchor` and `scaleratio` or those of the other axis), determines which direction we push the originally specified plot area. Options are "left", "center" (default), and "right" for x axes, and "top", "middle" (default), and "bottom" for y axes. Type: enumerated , one of ( `"left"` | `"center"` | `"right"` | `"top"` | `"middle"` | `"bottom"` )
* `dividercolor::String` - Sets the color of the dividers Only has an effect on "multicategory" axes. Type: color | Default: `"#444"`
* `dividerwidth::Float` - Sets the width (in px) of the dividers Only has an effect on "multicategory" axes. Type: float | Default: `1`
* `domain::Vector{Float64}` - Sets the domain of this axis (in plot fraction). Type: Vector
* `dtick::Union{Float64,Int,String}` - Sets the step in-between ticks on this axis. Use with `tick0`. Must be a positive number, or special strings available to "log" and "date" axes. If the axis `type` is "log", then ticks are set every 10^(n"dtick) where n is the tick number. For example, to set a tick mark at 1, 10, 100, 1000, ... set dtick to 1. To set tick marks at 1, 100, 10000, ... set dtick to 2. To set tick marks at 1, 5, 25, 125, 625, 3125, ... set dtick to log_10(5), or 0.69897000433. "log" has several special values; "L<f>", where `f` is a positive number, gives ticks linearly spaced in value (but not position). For example `tick0` = 0.1, `dtick` = "L0.5" will put ticks at 0.1, 0.6, 1.1, 1.6 etc. To show powers of 10 plus small digits between, use "D1" (all digits) or "D2" (only 2 and 5). `tick0` is ignored for "D1" and "D2". If the axis `type` is "date", then you must convert the time to milliseconds. For example, to set the interval between ticks to one day, set `dtick` to 86400000.0. "date" also has special values "M<n>" gives ticks spaced by a number of months. `n` must be a positive integer. To set ticks on the 15th of every third month, set `tick0` to "2000-01-15" and `dtick` to "M3". To set ticks every 4 years, set `dtick` to "M48"
* `fixedrange::Bool` - Determines whether or not this axis is zoom-able. If true, then zoom is disabled.
* `font::Font` - Check Font structure for signature.
* `gridcolor::String` - Sets the color of the grid lines. Type: color | Default: `"#eee"`
* `gridwidth::Int` - Sets the width (in px) of the grid lines. Type: float | Default: `1`
* `hoverformat::String` - Sets the hover text formatting rule using d3 formatting mini-languages which are very similar to those in Python. For numbers, see: https://github.com/d3/d3-format/tree/v1.4.5#d3-format. And for dates see: https://github.com/d3/d3-time-format/tree/v2.2.3#locale_format. We add two items to d3's date formatter: "%h" for half of the year as a decimal number as well as "%{n}f" for fractional seconds with n digits. For example, "2016-10-13 09:15:23.456" with tickformat "%H~%M~%S.%2f" would display "09~15~23.46". Default: `""`
* `layer::String` - Sets the layer on which this axis is displayed. If "above traces", this axis is displayed above all the subplot's traces If "below traces", this axis is displayed below all the subplot's traces, but above the grid lines. Useful when used together with scatter-like traces with `cliponaxis` set to "false" to show markers and/or text nodes above this axis. Type: enumerated , one of ( `"above traces"` | `"below traces"` ) | Default: `"above traces"`
* `linecolor::String` - Sets the axis line color. Type: color | Default: `"#444"`
* `linewidth::Int` - Sets the width (in px) of the axis line. Type: float | Default: `1`
* `minexponent::Int` - Hide SI prefix for 10^n if |n| is below this number. This only has an effect when `tickformat` is "SI" or "B". Type: number greater than or equal to `0` | Default: `3`
* `mirror::Union{Bool,String}` - Determines if the axis lines or/and ticks are mirrored to the opposite side of the plotting area. If "true", the axis lines are mirrored. If "ticks", the axis lines and ticks are mirrored. If "false", mirroring is disable. If "all", axis lines are mirrored on all shared-axes subplots. If "allticks", axis lines and ticks are mirrored on all shared-axes subplots. Type: `enumerated , one of ( `true` | `"ticks"` | `false` | `"all"` | `"allticks"` )`
* `nticks::Int` - Specifies the maximum number of ticks for the particular axis. The actual number of ticks will be chosen automatically to be less than or equal to `nticks`. Has an effect only if `tickmode` is set to "auto". Type: number greater than or equal to `0` | Default: `0`
* `overlaying::String` - If set a same-letter axis id, this axis is overlaid on top of the corresponding same-letter axis, with traces and axes visible for both axes. If "false", this axis does not overlay any same-letter axes. In this case, for axes with overlapping domains only the highest-numbered axis will be visible. Type: enumerated , one of ( `"free"` | `"/^x([2-9]|[1-9][0-9]+)?( domain)?\$/"` | `"/^y([2-9]|[1-9][0-9]+)?( domain)?\$/"` )
* `position::Float64` - Sets the position of this axis in the plotting space (in normalized coordinates). Only has an effect if `anchor` is set to "free". Type: number between or equal to `0` and `1` | Default: `0`
* `range::Union{Vector{Int},Vector{Float64}}` - Sets the range of this axis. If the axis `type` is "log", then you must take the log of your desired range (e.g. to set the range from 1 to 100, set the range from 0 to 2). If the axis `type` is "date", it should be date strings, like date data, though Date objects and unix milliseconds will be accepted and converted to strings. If the axis `type` is "category", it should be numbers, using the scale where each category is assigned a serial number from zero in the order it appears.
* `rangemode::String` - If "normal", the range is computed in relation to the extrema of the input data. If "tozero"`, the range extends to 0, regardless of the input data If "nonnegative", the range is non-negative, regardless of the input data. Applies only to linear axes. Type: enumerated , one of ( `"normal"` | `"tozero"` | `"nonnegative"` ) | Default: `"normal"`
* `scaleanchor::String` - If set to another axis id (e.g. `x2`, `y`), the range of this axis changes together with the range of the corresponding axis such that the scale of pixels per unit is in a constant ratio. Both axes are still zoomable, but when you zoom one, the other will zoom the same amount, keeping a fixed midpoint. `constrain` and `constraintoward` determine how we enforce the constraint. You can chain these, ie `yaxis: {scaleanchor: "x"}, xaxis2: {scaleanchor: "y"}` but you can only link axes of the same `type`. The linked axis can have the opposite letter (to constrain the aspect ratio) or the same letter (to match scales across subplots). Loops (`yaxis: {scaleanchor: "x"}, xaxis: {scaleanchor: "y"}` or longer) are redundant and the last constraint encountered will be ignored to avoid possible inconsistent constraints via `scaleratio`. Note that setting axes simultaneously in both a `scaleanchor` and a `matches` constraint is currently forbidden. Type: enumerated , one of ( `"/^x([2-9]|[1-9][0-9]+)?( domain)?\$/"` | `"/^y([2-9]|[1-9][0-9]+)?( domain)?\$/"` )
* `scaleratio::Int` - If this axis is linked to another by `scaleanchor`, this determines the pixel to unit scale ratio. For example, if this value is 10, then every unit on this axis spans 10 times the number of pixels as a unit on the linked axis. Use this for example to create an elevation profile where the vertical scale is exaggerated a fixed amount with respect to the horizontal. Type: number greater than or equal to `0` | Default: `1`
* `showdividers::Bool` - Determines whether or not a dividers are drawn between the category levels of this axis. Only has an effect on "multicategory" axes. Type: boolean | Default: `true`
* `showexponent::String` - If "all", all exponents are shown besides their significands. If "first", only the exponent of the first tick is shown. If "last", only the exponent of the last tick is shown. If "none", no exponents appear. Type: enumerated , one of ( `"all"` | `"first"` | `"last"` | `"none"` ) | Default: `"all"`
* `showgrid::Bool` - Determines whether or not grid lines are drawn. If True, the grid lines are drawn at every tick mark. Type: boolean | Default: `true`
* `showline::Bool` - Determines whether or not a line bounding this axis is drawn. Type: boolean
* `showspikes::Bool` - Determines whether or not spikes (aka droplines) are drawn for this axis. Note: This only takes affect when hovermode = closest. Type: boolean
* `showticklabels::Bool` - Determines whether or not the tick labels are drawn.
* `side::String` - Determines whether a x (y) axis is positioned at the "bottom" ("left") or "top" ("right") of the plotting area. Type: enumerated , one of ( `"top"` | `"bottom"` | `"left"` | `"right"` ) | Default: `"bottom"`
* `spikecolor::String` - Sets the spike color. If undefined, will use the series color
* `spikedash::String` - Sets the dash style of lines. Set to a dash type string ("solid", "dot", "dash", "longdash", "dashdot", or "longdashdot") or a dash length list in px (eg "5px,10px,2px,2px").
* `spikemode::String` - Determines the drawing mode for the spike line If "toaxis", the line is drawn from the data point to the axis the series is plotted on. If "across", the line is drawn across the entire plot area, and supercedes "toaxis". If "marker", then a marker dot is drawn on the axis the series is plotted on. Type: Any combination of `"toaxis"`, `"across"`, `"marker"` joined with a `"+"` | Examples. `"toaxis"` | `"across"` | `"marker"` | `"toaxis+across"` | `"toaxis+marker"` | `"across+marker"` | `"toaxis+across+marker"` | Default: `"toaxis"`
* `spikesnap::String` - Determines whether spikelines are stuck to the cursor or to the closest datapoints. Type: enumerated , one of ( `"data"` | `"cursor"` | `"hovered data"`) | Default: `"hovered data"`
* `spikethickness::Int` - Sets the width (in px) of the zero line. Default: 3
* `tick0::Union{Float64,Int,String}` - Sets the placement of the first tick on this axis. Use with `dtick`. If the axis `type` is "log", then you must take the log of your starting tick (e.g. to set the starting tick to 100, set the `tick0` to 2) except when `dtick`="L<f>" (see `dtick` for more info). If the axis `type` is "date", it should be a date string, like date data. If the axis `type` is "category", it should be a number, using the scale where each category is assigned a serial number from zero in the order it appears.
* `tickangle::Union{String,Int,Float64}` - Sets the angle of the tick labels with respect to the horizontal. For example, a `tickangle` of -90 draws the tick labels vertically. Default: `"auto"`
* `tickcolor::String` - Sets the tick color. Default: `"#444"`
* `tickformat::String` - Sets the tick label formatting rule using d3 formatting mini-languages which are very similar to those in Python. For numbers, see: https://github.com/d3/d3-format/tree/v1.4.5#d3-format. And for dates see: https://github.com/d3/d3-time-format/tree/v2.2.3#locale_format. We add two items to d3's date formatter: "%h" for half of the year as a decimal number as well as "%{n}f" for fractional seconds with n digits. For example, "2016-10-13 09:15:23.456" with tickformat "%H~%M~%S.%2f" would display "09~15~23.46". Default: `""`
* `ticklabelmode::String` - Determines where tick labels are drawn with respect to their corresponding ticks and grid lines. Only has an effect for axes of `type` "date" When set to "period", tick labels are drawn in the middle of the period between ticks. Type: enumerated , one of ( `"instant"` | `"period"` ) | Default: `"instant"`
* `ticklabeloverflow::String` - Determines how we handle tick labels that would overflow either the graph div or the domain of the axis. The default value for inside tick labels is "hide past domain". Otherwise on "category" and "multicategory" axes the default is "allow". In other cases the default is "hide past div". Type: enumerated , one of ( `"allow"` |` "hide past div"` | `"hide past domain"` )
* `ticklabelposition::String` - Determines where tick labels are drawn with respect to the axis Please note that top or bottom has no effect on x axes or when `ticklabelmode` is set to "period". Similarly left or right has no effect on y axes or when `ticklabelmode` is set to "period". Has no effect on "multicategory" axes or when `tickson` is set to "boundaries". When used on axes linked by `matches` or `scaleanchor`, no extra padding for inside labels would be added by autorange, so that the scales could match. Type: enumerated , one of ( `"top"` | `"bottom"` | `"left"` | `"right"` | `"outsideleft"` | `"insideleft"` ) | Default: `"outside"`
* `ticklen::Int` - Sets the tick length (in px). Default: `5`
* `tickmode::String` - Sets the tick mode for this axis. If "auto", the number of ticks is set via `nticks`. If "linear", the placement of the ticks is determined by a starting position `tick0` and a tick step `dtick` ("linear" is the default value if `tick0` and `dtick` are provided). If "array", the placement of the ticks is set via `tickvals` and the tick text is `ticktext`. ("array" is the default value if `tickvals` is provided). Type: enumerated , one of ( `"auto"` | `"linear"` | `"array"` )
* `tickprefix::String` - Sets a tick label prefix. Default: `""`
* `ticks::String` - Determines whether ticks are drawn or not. If "", this axis' ticks are not drawn. If "outside" ("inside"), this axis' are drawn outside (inside) the axis lines.
* `tickson::String` - Determines where ticks and grid lines are drawn with respect to their corresponding tick labels. Only has an effect for axes of `type` "category" or "multicategory". When set to "boundaries", ticks and grid lines are drawn half a category to the left/bottom of labels. Type: enumerated , one of (`"labels"` | `"boundaries"` ) | Default: `"labels"`
* `ticksuffix::String` - Sets a tick label suffix. Default: `""`
* `ticktext::Vector{String}` - Sets the text displayed at the ticks position via `tickvals`. Only has an effect if `tickmode` is set to "array". Used with `tickvals`.
* `tickvals::Union{Vector{Float64},Vector{Int}}` - Sets the values at which ticks on this axis appear. Only has an effect if `tickmode` is set to "array". Used with `ticktext`.
* `tickwidth::Int` - Sets the tick width (in px). Type: number greater than or equal to `0` | Default: `1`
* `title::String` - Sets the title of this axis.
* `type::String` - Sets the axis type. By default, plotly attempts to determined the axis type by looking into the data of the traces that referenced the axis in question. Type: enumerated , one of ( `"-"` | `"linear"` | `"log"` | `"date"` | `"category"` | `"multicategory"` ) | Default: `"-"`
* `visible::Bool` - A single toggle to hide the axis while preserving interaction like dragging. Default is true when a cheater plot is present on the axis, otherwise false
* `zeroline::Bool` - Determines whether or not a line is drawn at along the 0 value of this axis. If "true", the zero line is drawn on top of the grid lines.
* `zerolinecolor::String` - Sets the line color of the zero line. Default: `#444`
* `zerolinewidth::Int` - Sets the width (in px) of the zero line. Default: `1`
#### Important
* `xy::String` - Sets a reference to the x or y axis. If "x", the `x` axis will be matched. If "y", the `y` axis will be matched.
* `index::Int` - 1 # 1, 2, 3 etc. for subplots
* `title_text::String` - Sets the text of the title of this axis.
* `title_font::Font` - Sets the title font.
* `title_standoff:Int` - Sets the standoff distance between the axis title and the axis labels, in pixels.
"""
Base.@kwdef mutable struct PlotLayoutAxis
anchor::Union{String,Nothing} = nothing
automargin::Union{Bool,Nothing} = nothing
autorange::Union{Bool,String,Nothing} = nothing
autotypenumbers::Union{String,Nothing} = nothing
calendar::Union{String,Nothing} = nothing
categoryarray::Union{Vector{Float64},Nothing} = nothing
categoryorder::Union{String,Nothing} = nothing
constrain::Union{String,Nothing} = nothing
constraintoward::Union{String,Nothing} = nothing
dividercolor::Union{String,Nothing} = nothing
dividerwidth::Union{Int,Nothing} = nothing
domain::Union{Vector{Float64},Nothing} = nothing
dtick::Union{Float64,Int,String,Nothing} = nothing
fixedrange::Union{Bool,Nothing} = nothing
font::Union{Font,Nothing} = nothing
gridcolor::Union{String,Nothing} = nothing
gridwidth::Union{Int,Nothing} = nothing
hoverformat::Union{String,Nothing} = nothing
layer::Union{String,Nothing} = nothing
linecolor::Union{String,Nothing} = nothing
linewidth::Union{Int,Nothing} = nothing
minexponent::Union{Int,Nothing} = nothing
mirror::Union{Bool,String,Nothing} = nothing
nticks::Union{Int,Nothing} = nothing
overlaying::Union{String,Nothing} = nothing
position::Union{Float64,Nothing} = nothing
range::Union{Vector{Int},Vector{Float64},Nothing} = nothing
rangemode::Union{String,Nothing} = nothing
scaleanchor::Union{String,Nothing} = nothing
scaleratio::Union{Int,Nothing} = nothing
showdividers::Union{Bool,Nothing} = nothing
showexponent::Union{String,Nothing} = nothing
showgrid::Union{Bool,Nothing} = nothing
showline::Union{Bool,Nothing} = nothing
showspikes::Union{Bool,Nothing} = nothing
showticklabels::Union{Bool,Nothing} = nothing
side::Union{String,Nothing} = nothing
spikecolor::Union{String,Nothing} = nothing
spikedash::Union{String,Nothing} = nothing
spikemode::Union{String,Nothing} = nothing
spikesnap::Union{String,Nothing} = nothing
spikethickness::Union{Int,Nothing} = nothing
tick0::Union{Float64,Int,String,Nothing} = nothing
tickangle::Union{String,Int,Float64,Nothing} = nothing
tickcolor::Union{String,Nothing} = nothing
tickfont::Union{Font,Nothing} = nothing
tickformat::Union{String,Nothing} = nothing
ticklabelmode::Union{String,Nothing} = nothing
ticklabelposition::Union{String,Nothing} = nothing
ticklen::Union{Int,Nothing} = nothing
tickmode::Union{String,Nothing} = nothing
tickprefix::Union{String,Nothing} = nothing
ticks::Union{String,Nothing} = nothing
tickson::Union{String,Nothing} = nothing
ticksuffix::Union{String,Nothing} = nothing
ticktext::Union{Vector{String},Nothing} = nothing
tickvals::Union{Vector{Float64},Vector{Int},Nothing} = nothing
tickwidth::Union{Int,Nothing} = nothing
title::Union{String,Nothing} = nothing # "axis title"
type::Union{String,Nothing} = nothing
visible::Union{Bool,Nothing} = nothing
zeroline::Union{Bool,Nothing} = nothing
zerolinecolor::Union{String,Nothing} = nothing
zerolinewidth::Union{Int,Nothing} = nothing
# needs special treatment
xy::String = "x" # "x" or "y"
index::Int = 1 # 1, 2, 3 etc. for subplots
title_text::Union{String,Nothing} = nothing
title_font::Union{Font,Nothing} = nothing
title_standoff::Union{Int,Nothing} = nothing
end
function Base.show(io::IO, la::PlotLayoutAxis)
output = "Layout Axis: \n"
for f in fieldnames(typeof(la))
prop = getproperty(la, f)
if prop !== nothing
output *= "$f = $prop \n"
end
end
print(io, output)
end
function Base.Dict(la::PlotLayoutAxis, xy::String = "")
trace = Dict{Symbol,Any}()
if la.title_text !== nothing
d = Dict{Symbol,Any}(:text => la.title_text)
(la.title_font !== nothing) && (d[:font] = la.title_font)
(la.title_standoff !== nothing) && (d[:standoff] = la.title_standoff)
trace[:title] = d
end
d = optionals!(trace, la, [
:anchor, :automargin, :autorange, :autotypenumbers, :calendar, :categoryarray,
:categoryorder, :constrain, :constraintoward, :dividercolor, :dividerwidth, :domain, :dtick,
:fixedrange, :font, :gridcolor, :gridwidth, :hoverformat, :layer, :linecolor, :linewidth,
:minexponent, :mirror, :nticks, :overlaying, :position, :range, :rangemode, :scaleanchor,
:scaleratio, :showdividers, :showexponent, :showgrid, :showline, :showspikes, :showticklabels,
:side, :spikecolor, :spikedash, :spikemode, :spikesnap, :spikethickness, :tick0, :tickangle,
:tickcolor, :tickfont, :tickformat, :ticklabelmode, :ticklabelposition, :ticklen, :tickmode,
:tickprefix, :ticks, :tickson, :ticksuffix, :ticktext, :tickvals, :tickwidth, :title, :type,
:visible, :zeroline, :zerolinecolor, :zerolinewidth])
k = Symbol(isempty(xy) ? la.xy : xy, "axis", la.index > 1 ? "$(la.index)" : "")
Dict(k => d)
end
function Stipple.render(la::PlotLayoutAxis, fieldname::Union{Symbol,Nothing} = nothing)
[Dict(la)]
end
function Stipple.render(lav::Vector{PlotLayoutAxis}, fieldname::Union{Symbol,Nothing} = nothing)
[Dict(la) for la in lav]
end
#===#
Base.@kwdef mutable struct PlotLayoutTitle
text::Union{String,Nothing} = nothing # ""
font::Union{Font,Nothing} = nothing # Font()
xref::Union{String,Nothing} = nothing # LAYOUT_TITLE_REF_CONTAINER
yref::Union{String,Nothing} = nothing # LAYOUT_TITLE_REF_CONTAINER
x::Union{Float64,String,Nothing} = nothing # 0.5
y::Union{Float64,String,Nothing} = nothing # LAYOUT_AUTO
xanchor::Union{String,Nothing} = nothing # LAYOUT_AUTO
yanchor::Union{String,Nothing} = nothing # LAYOUT_AUTO
pad_t::Union{Int,Nothing} = nothing # 0
pad_r::Union{Int,Nothing} = nothing # 0
pad_b::Union{Int,Nothing} = nothing # 0
pad_l::Union{Int,Nothing} = nothing # 0
end
function Base.show(io::IO, plt::PlotLayoutTitle)
output = "Layout Title: \n"
for f in fieldnames(typeof(plt))
prop = getproperty(plt, f)
if prop !== nothing
output *= "$f = $prop \n"
end
end
print(io, output)
end
function Base.Dict(plt::PlotLayoutTitle)
trace = Dict{Symbol, Any}()
d = Dict{Symbol, Any}()
(plt.pad_t !== nothing) && (d[:t] = plt.pad_t)
(plt.pad_r !== nothing) && (d[:r] = plt.pad_r)
(plt.pad_b !== nothing) && (d[:b] = plt.pad_b)
(plt.pad_l !== nothing) && (d[:l] = plt.pad_l)
(length(d) > 0) && (trace[:pad] = d)
optionals!(trace, plt, [:text, :font, :xref, :yref, :x, :y, :xanchor, :yanchor])
end
function Stipple.render(plt::PlotLayoutTitle, fieldname::Union{Symbol,Nothing} = nothing)
Dict(plt)
end
#===#
"""
PlotLayoutLegend()
----------
# Examples
----------
```
julia>
```
-----------
# Properties
-----------
* `bgcolor::String` - Sets the legend background color. Defaults to `layout.paper_bgcolor`. Type: `color`
* `bordercolor::String` - Sets the color of the border enclosing the legend. Type: `color` | Default: `"#444"`
* `borderwidth::Int` - Sets the width (in px) of the border enclosing the legend. Type: `int` | Default: `0`
* `font::Font` - Sets the font used to text the legend items. Type: `Font` | Default: `Font()`
* `itemclick::Union{String,Bool}` - Determines the behavior on legend item click. "toggle" toggles the visibility of the item clicked on the graph. "toggleothers" makes the clicked item the sole visible item on the graph. "false" disables legend item click interactions. Type: enumerated , one of ( `"toggle"` | `"toggleothers"` | `false` ) | Default: `"toggle"`
* `itemdoubleclick::Union{String,Bool}` - Determines the behavior on legend item double-click. "toggle" toggles the visibility of the item clicked on the graph. "toggleothers" makes the clicked item the sole visible item on the graph. "false" disables legend item double-click interactions. Type: enumerated , one of ( `"toggle"` | `"toggleothers"` | `false` ) | Default: `"toggleothers"`
* `itemsizing::String` - Determines if the legend items symbols scale with their corresponding "trace" attributes or remain "constant" independent of the symbol size on the graph. Type: enumerated , one of ( `"trace"` | `"constant"` ) | Default: `"trace"`
* `itemwidth::Int` - Sets the width (in px) of the legend item symbols (the part other than the title.text). Type: `int` | Default: `30`
* `orientation::String` - Sets the orientation of the legend. Type: enumerated , one of ( `"v"` | `"h"` ) | Default: `"v"`
* `title_text::String` - Sets the text of the legend's title. Type: `String`
* `title_font::Font` - Sets the font used for the legend's title. Type: `Font`
* `title_side::String` - Sets the side of the legend.
* `tracegroupgap::Int` - Sets the amount of vertical space (in px) between legend groups. Type: number greater than or equal to `0` | Default: `10`
* `traceorder::String` - Determines the order at which the legend items are displayed. If "normal", the items are displayed top-to-bottom in the same order as the input data. If "reversed", the items are displayed in the opposite order as "normal". If "grouped", the items are displayed in groups (when a trace `legendgroup` is provided). if "grouped+reversed", the items are displayed in the opposite order as "grouped". Type: flaglist string. Any combination of `"reversed"`, `"grouped"` joined with a `"+"` OR `"normal"`. | Examples: Examples: `"reversed"`, `"grouped"`, `"reversed+grouped"`, `"normal"`
* `valign::String` - Sets the vertical alignment of the symbols with respect to their associated text. Type: enumerated , one of ( `"top"` | `"middle"` | `"bottom"` ) | Default: `"middle"`
* `x::Union{Int,Float64}` - Sets the x position (in normalized coordinates) of the legend. Defaults to "1.02" for vertical legends and defaults to "0" for horizontal legends. Type: number between or equal to `-2` and `3`
* `xanchor::String` - Sets the legend's horizontal position anchor. This anchor binds the `x` position to the "left", "center" or "right" of the legend. Value "auto" anchors legends to the right for `x` values greater than or equal to 2/3, anchors legends to the left for `x` values less than or equal to 1/3 and anchors legends with respect to their center otherwise. Type: enumerated , one of ( `"left"` | `"center"` | `"right"` | `"auto"` ) | Default: `"left"`
* `y::Union{Int,Float64}` - Sets the y position (in normalized coordinates) of the legend. Defaults to "1" for vertical legends, defaults to "-0.1" for horizontal legends on graphs w/o range sliders and defaults to "1.1" for horizontal legends on graph with one or multiple range sliders. Type: number between or equal to `-2` and `3`
* `yanchor::String` - Sets the legend's vertical position anchor This anchor binds the `y` position to the "top", "middle" or "bottom" of the legend. Value "auto" anchors legends at their bottom for `y` values less than or equal to 1/3, anchors legends to at their top for `y` values greater than or equal to 2/3 and anchors legends with respect to their middle otherwise. Type: enumerated , one of ( `"top"` | `"middle"` | `"bottom"` | `"auto"` )
"""
Base.@kwdef mutable struct PlotLayoutLegend
bgcolor::Union{String,Nothing} = nothing
bordercolor::Union{String,Nothing} = nothing # "#444"
borderwidth::Union{Int,Nothing} = nothing # 0
font::Union{Font,Nothing} = nothing # Font()
itemclick::Union{String,Bool,Nothing} = nothing # LAYOUT_CLICK_TOGGLE
itemdoubleclick::Union{String,Bool,Nothing} = nothing # LAYOUT_CLICK_TOGGLEOTHERS
itemsizing::Union{String,Nothing} = nothing # LAYOUT_ITEMSIZING_TRACE
itemwidth::Union{Int,Nothing} = nothing # 30
orientation::Union{String,Nothing} = nothing # LAYOUT_ORIENTATION_VERTICAL
title_text::Union{String,Nothing} = nothing # ""
title_font::Union{Font,Nothing} = nothing # Font()
title_side::Union{String,Nothing} = nothing # LAYOUT_LEFT
tracegroupgap::Union{Int,Nothing} = nothing # 10
traceorder::Union{String,Nothing} = nothing # "normal"
valign::Union{String,Nothing} = nothing # LAYOUT_MIDDLE
x::Union{Int,Float64,Nothing} = nothing # 1.02
xanchor::Union{String,Nothing} = nothing # LAYOUT_LEFT
y::Union{Int,Float64,Nothing} = nothing # 1
yanchor::Union{String,Nothing} = nothing # LAYOUT_AUTO
# TODO: uirevision::Union{Int,String} = ""
end
function Base.show(io::IO, pll::PlotLayoutLegend)
output = "Layout Legend: \n"
for f in fieldnames(typeof(pll))
prop = getproperty(pll, f)
if prop !== nothing
output *= "$f = $prop \n"
end
end
print(io, output)
end
function Base.Dict(pll::PlotLayoutLegend)
trace = Dict{Symbol, Any}()
d = Dict{Symbol, Any}()
(pll.title_text !== nothing) && (d[:text] = pll.title_text)
(pll.title_font !== nothing) && (d[:font] = pll.title_font)
(pll.title_side !== nothing) && (d[:side] = pll.title_side)
(length(d) > 0) && (trace[:title] = d)
optionals!(trace, pll, [
:bgcolor, :bordercolor, :borderwidth, :font, :orientation, :tracegroupgap, :traceorder,
:itemsizing, :itemwidth, :itemclick, :itemdoubleclick, :x, :xanchor, :y, :yanchor, :valign])
end
function Stipple.render(pll::PlotLayoutLegend, fieldname::Union{Symbol,Nothing} = nothing)
Dict(pll)
end
#===#
"""
PlotLayoutGrid()
----------
# Examples
----------
```
julia>
```
-----------
# Properties
-----------
* `columns::String` - The number of columns in the grid. If you provide a 2D `subplots` array, the length of its longest row is used as the default. If you give an `xaxes` array, its length is used as the default. But it's also possible to have a different length, if you want to leave a row at the end for non-cartesian subplots. Type: integer greater than or equal to `1`
* `domain_x::Vector{Float64}` - Sets the horizontal domain of this grid subplot (in plot fraction). The first and last cells end exactly at the domain edges, with no grout around the edges. Default: `[0, 1]`
* `domain_y::Vector{Float64}` - Sets the vertical domain of this grid subplot (in plot fraction). The first and last cells end exactly at the domain edges, with no grout around the edges. Default: `[0, 1]`
* `pattern::String` - If no `subplots`, `xaxes`, or `yaxes` are given but we do have `rows` and `columns`, we can generate defaults using consecutive axis IDs, in two ways: "coupled" gives one x axis per column and one y axis per row. "independent" uses a new xy pair for each cell, left-to-right across each row then iterating rows according to `roworder`. Type: one of `"coupled"` or `"independent"` | Default. `"coupled"`
* `roworder::String` - Is the first row the top or the bottom? Note that columns are always enumerated from left to right. enumerated , one of ( `"top to bottom"` | `"bottom to top"` ) | Default: `"top to bottom"`
* `rows::Int` - The number of rows in the grid. If you provide a 2D `subplots` array or a `yaxes` array, its length is used as the default. But it's also possible to have a different length, if you want to leave a row at the end for non-cartesian subplots. Type: integer greater than or equal to `1`
* `subplots::Matrix{String}` - Used for freeform grids, where some axes may be shared across subplots but others are not. Each entry should be a cartesian subplot id, like "xy" or "x3y2", or "" to leave that cell empty. You may reuse x axes within the same column, and y axes within the same row. Non-cartesian subplots and traces that support `domain` can place themselves in this grid separately using the `gridcell` attribute.
* `xaxes::Vector{String}` - Used with `yaxes` when the x and y axes are shared across columns and rows. Each entry should be an x axis id like "x", "x2", etc., or "" to not put an x axis in that column. Entries other than "" must be unique. Ignored if `subplots` is present. If missing but `yaxes` is present, will generate consecutive IDs.
* `xgap::Float64` - Horizontal space between grid cells, expressed as a fraction of the total width available to one cell. Defaults to 0.1 for coupled-axes grids and 0.2 for independent grids. Type: number between or equal to `0` and `1`
* `xside::String` - Sets where the x axis labels and titles go. "bottom" means the very bottom of the grid. "bottom plot" is the lowest plot that each x axis is used in. "top" and "top plot" are similar. Type: enumerated , one of ( `"bottom"` | `"bottom plot"` | `"top plot"` | `"top"` ) | Default: `"bottom plot"`
* `yaxes::Vector{String}` - Used with `yaxes` when the x and y axes are shared across columns and rows. Each entry should be an y axis id like "y", "y2", etc., or "" to not put a y axis in that row. Entries other than "" must be unique. Ignored if `subplots` is present. If missing but `xaxes` is present, will generate consecutive IDs.
* `ygap::Float64` - Vertical space between grid cells, expressed as a fraction of the total height available to one cell. Defaults to 0.1 for coupled-axes grids and 0.3 for independent grids. Type: number between or equal to `0` and `1`
* `yside::String` - Sets where the y axis labels and titles go. "left" means the very left edge of the grid. "left plot" is the leftmost plot that each y axis is used in. "right" and "right plot" are similar. Type: enumerated , one of ( `"left"` | `"left plot"` | `"right plot"` | `"right"` ) | Default: `"left plot"`
"""
Base.@kwdef mutable struct PlotLayoutGrid
columns::Union{Int,Nothing} = nothing # >= 1
domain_x::Union{Vector{Float64},Nothing} = nothing # fraction, e.g [0, 1]
domain_y::Union{Vector{Float64},Nothing} = nothing # fraction, e.g [0, 1]
pattern::Union{String,Nothing} = nothing # "independent" | "coupled"
roworder::Union{String,Nothing} = nothing # "top to bottom" | "bottom to top"
rows::Union{Int,Nothing} = nothing # >= 1
subplots::Union{Matrix{String},Nothing} = nothing
xaxes::Union{Vector{String},Nothing} = nothing
xgap::Union{Float64,Nothing} = nothing # [0.0, 1.0]
xside::Union{String,Nothing} = nothing # "bottom" | "bottom plot" | "top plot" | "top"
yaxes::Union{Vector{String},Nothing} = nothing
ygap::Union{Float64,Nothing} = nothing # [0.0, 1.0]
yside::Union{String,Nothing} = nothing # "bottom" | "bottom plot" | "top plot" | "top"
end
function Base.show(io::IO, lg::PlotLayoutGrid)
output = "Layout Grid: \n"
for f in fieldnames(typeof(lg))
prop = getproperty(lg, f)
if prop !== nothing
output *= "$f = $prop \n"
end
end
print(io, output)
end
function Base.Dict(lg::PlotLayoutGrid)
trace = Dict{Symbol,Any}()
if (lg.domain_x !== nothing) & (lg.domain_y !== nothing)
trace[:domain] = Dict(
:x => lg.domain_x,
:y => lg.domain_y
)
elseif lg.domain_x !== nothing
trace[:domain] = Dict(
:x => lg.domain_x
)
elseif lg.domain_y !== nothing
trace[:domain] = Dict(
:y => lg.domain_y
)
end
optionals!(trace, lg, [:columns, :domain_x, :domain_y, :pattern, :roworder,
:rows, :subplots, :xaxes, :xgap, :xside, :yaxes, :ygap, :yside])
end
#===#
"""
GeoProjection()
----------
# Examples
----------
```
julia>
```
-----------
# Properties
-----------
* `distance::Float64` - For satellite projection type only. Sets the distance from the center of the sphere to the point of view as a proportion of the sphere’s radius. Type: number greater than or equal to `1.001` | Default: `2`
* `parallels::Vector{Float64}` - For conic projection types only. Sets the parallels (tangent, secant) where the cone intersects the sphere.
* `rotation::Protation` - Check Protation struct for more details
* `scale::Float64` - Zooms in or out on the map view. A scale of "1" corresponds to the largest zoom level that fits the map's lon and lat ranges. number greater than or equal to `0` | Default: `1`
* `tilt::Float64` - For satellite projection type only. Sets the tilt angle of perspective projection. Type: `number` | Default: `0`
* `type::String` - Sets the projection type. Type: enumerated , one of ( `"albers"` | `"albers usa"` | `"azimuthal equal area"` | `"azimuthal equidistant"` | `"conic equal area"` | `"conic conformal"` | `"conic equidistant"` | `"equidistant conic"` | `"gnomonic"` | `"mercator"` | `"natural earth"` | `"orthographic"` | `"stereographic"` | `"transverse mercator"` )
"""
Base.@kwdef mutable struct GeoProjection
distance::Union{Float64,Nothing} = nothing
parallels::Union{Vector{Float64},Nothing} = nothing
rotation::Union{Protation, Nothing} = nothing
scale::Union{Float64,Nothing} = nothing
tilt::Union{Float64,Nothing} = nothing
type::Union{String,Nothing} = nothing
end
function Base.show(io::IO, proj::GeoProjection)
output = "Geo Layout Projection: \n"
for f in fieldnames(typeof(proj))
prop = getproperty(proj, f)
if prop !== nothing
output *= "$f = $prop \n"
end
end
print(io, output)
end
function Base.Dict(proj::GeoProjection)
trace = Dict{Symbol, Any}()
optionals!(trace, proj, [:distance, :parallels, :rotation, :scale, :tilt, :type])
end
function Stipple.render(proj::GeoProjection, fieldname::Union{Symbol,Nothing} = nothing)
Dict(proj)
end
"""
PlotLayoutGeo()
----------
# Examples
----------
```
julia>
```
-----------
# Properties
-----------
* `bgcolor::String` - Set the background color of the map. Type: `color` | Default: `"#fff"`
* `center::Mcenter` - Check Mcenter documentation for details.
* `coastlinecolor::String` - Set the coastline color. Type: `color` | Default: `"#444"`
* `coastlinewidth::Int` - Set the coastline width. Type: `number` | Default: `1`
* `countrywidth::Int` - Sets line color of the country boundaries. Type: number greater than or equal to `0` | Default: `1`
* `fitbounds::Bool` - Determines if this subplot's view settings are auto-computed to fit trace data. On scoped maps, setting `fitbounds` leads to `center.lon` and `center.lat` getting auto-filled. On maps with a non-clipped projection, setting `fitbounds` leads to `center.lon`, `center.lat`, and `projection.rotation.lon` getting auto-filled. On maps with a clipped projection, setting `fitbounds` leads to `center.lon`, `center.lat`, `projection.rotation.lon`, `projection.rotation.lat`, `lonaxis.range` and `lonaxis.range` getting auto-filled. If "locations", only the trace's visible locations are considered in the `fitbounds` computations. If "geojson", the entire trace input `geojson` (if provided) is considered in the `fitbounds` computations, Defaults to "false". Type: enumerated , one of ( false | "locations" | "geojson" )
* `framecolor::String` - Set the frame color. Type: `color` | Default: `"#444"`
* `framewidth::Int` - Sets the stroke width (in px) of the frame. Type: number greater than or equal to `0` | Default: `1`
* `lakecolor::String` - Set the color of the lakes. Type: `color` | Default: `"#3399FF"`
* `landcolor::String` - Sets the land mass color. Type: `color` | Default: `"#F0DC82"`
* `lataxis::PlotLayoutAxis` - Check PlotLayoutAxis documentation for details.
* `lonaxis::PlotLayoutAxis` - Check PlotLayoutAxis documentation for details.
* `oceancolor::String` - Sets the ocean color. Type: `color` | Default: `"#3399FF"`
* `geoprojection::GeoProjection` - Check GeoProjection documentation for details.
* `resolution::String` - Sets the resolution of the base layers. The values have units of km/mm e.g. 110 corresponds to a scale ratio of `1:110,000,000`. Type: enumerated , one of ( `"110"` | `"50"` ) | Default: `"110"`
* `rivercolor::String` - Sets color of the rivers. Type: `color` | Default: `"#3399FF"`
* `riverwidth::Int` - Sets the stroke width (in px) of the rivers. Type: number greater than or equal to `0` | Default: `1`
* `scope::String` - Sets the scope of the map. Type: enumerated , one of ( `"world"` | `"usa"` | `"europe"` | `"asia"` | `"africa"` | `"north america"` | `"south america"` ) | Default: `"world"`
* `showcoastlines::Bool` - Sets whether or not the coastlines are drawn.
* `showcountries::Bool` - Sets whether or not country boundaries are drawn.
* `showframe::Bool` - Sets whether or not a frame is drawn around the map.
* `showlakes::Bool` - Sets whether or not lakes are drawn.
* `showland::Bool` - Sets whether or not land masses are filled in color.
* `showocean::Bool` - Sets whether or not oceans are filled in color.
* `showrivers::Bool` - Sets whether or not rivers are drawn.
* `showsubunits::Bool` - Sets whether or not boundaries of subunits within countries (e.g. states, provinces) are drawn.
* `subunitcolor::String` - Sets the color of the subunits boundaries. Type: `color` | Default: `"#444"`
* `subunitwidth::Int` - Sets the stroke width (in px) of the subunits boundaries. Type: number greater than or equal to `0` | Default: `1`
* `uirevision::Union{String,Int}` - Controls persistence of user-driven changes in the view (projection and center). Defaults to `layout.uirevision`. Type: number or categorical coordinate string
* `visible::Bool` - Sets the default visibility of the base layers. Default: `true`
"""
Base.@kwdef mutable struct PlotLayoutGeo
bgcolor::Union{String, Nothing} = nothing # ""
center::Union{Mcenter, Nothing} = nothing # MCenter(0, 0)
coastlinecolor::Union{String, Nothing} = nothing # ""
coastlinewidth::Union{Int, Nothing} = nothing # 1
countrycolor::Union{String, Nothing} = nothing # ""
countrywidth::Union{Int, Nothing} = nothing # 1
fitbounds::Union{Bool, Nothing} = nothing # false
framecolor::Union{String, Nothing} = nothing # ""
framewidth::Union{Int, Nothing} = nothing # 0
lakecolor::Union{String, Nothing} = nothing # ""
landcolor::Union{String, Nothing} = nothing # ""
lataxis::Union{PlotLayoutAxis,Nothing} = nothing
lonaxis::Union{PlotLayoutAxis,Nothing} = nothing
oceancolor::Union{String, Nothing} = nothing # ""
geoprojection::Union{GeoProjection, Nothing} = nothing
resolution::Union{String, Nothing} = nothing # 50
rivercolor::Union{String, Nothing} = nothing # ""
riverwidth::Union{Int, Nothing} = nothing # 1
scope::Union{String, Nothing} = nothing # "world"
showcoastlines::Union{Bool, Nothing} = nothing # true
showcountries::Union{Bool, Nothing} = nothing # true
showframe::Union{Bool, Nothing} = nothing # false
showlakes::Union{Bool, Nothing} = nothing # true
showland::Union{Bool, Nothing} = nothing # true
showocean::Union{Bool, Nothing} = nothing # true
showrivers::Union{Bool, Nothing} = nothing # true
showsubunits::Union{Bool, Nothing} = nothing # true
subunitcolor::Union{String, Nothing} = nothing # ""
subunitwidth::Union{Int, Nothing} = nothing # 1
uirevision::Union{Int, String, Nothing} = nothing # "number or categorical coordinate string
visible::Union{Bool, Nothing} = nothing # true
end
function Base.show(io::IO, geo::PlotLayoutGeo)
output = "Layout Geo: \n"
for f in fieldnames(typeof(geo))
prop = getproperty(geo, f)
if prop !== nothing
output *= "$f = $prop \n"
end
end
print(io, output)
end
function Base.Dict(geo::PlotLayoutGeo)
trace = Dict{Symbol, Any}()
optionals!(trace, geo, [
:bgcolor, :center, :coastlinecolor, :coastlinewidth, :countrycolor, :countrywidth,
:fitbounds, :framecolor, :framewidth, :lakecolor, :landcolor, :oceancolor, :geoprojection,
:resolution, :rivercolor, :riverwidth, :scope, :showcoastlines, :showcountries, :showframe,
:showlakes, :showland, :showocean, :showrivers, :showsubunits, :subunitcolor, :subunitwidth,
:uirevision, :visible])
end
function Stipple.render(geo::PlotLayoutGeo, fieldname::Union{Symbol,Nothing} = nothing)
Dict(geo)
end
#===#
Base.@kwdef mutable struct PlotLayoutMapbox
style::Union{String, Nothing} = nothing # "open-street-map"
zoom::Union{Float64, Nothing} = nothing # 0
center::Union{Mcenter, Nothing} = nothing # MCenter(0, 0)
end
function Base.show(io::IO, mapbox::PlotLayoutMapbox)
output = "Layout Geo: \n"
for f in fieldnames(typeof(mapbox))
prop = getproperty(mapbox, f)
if prop !== nothing
output *= "$f = $prop \n"
end
end
print(io, output)
end
function Base.Dict(mapbox::PlotLayoutMapbox)
trace = Dict{Symbol, Any}()
optionals!(trace, geo, [:style, :zoom, :center])
end
function Stipple.render(mapbox::PlotLayoutMapbox, fieldname::Union{Symbol,Nothing} = nothing)
Dict(map)
end
#===#
Base.@kwdef mutable struct PlotLayout
title::Union{PlotLayoutTitle,Nothing} = nothing
xaxis::Union{Vector{PlotLayoutAxis},Nothing} = nothing
yaxis::Union{Vector{PlotLayoutAxis},Nothing} = nothing
axes::Union{Vector{PlotLayoutAxis},Nothing} = nothing
showlegend::Union{Bool,Nothing} = nothing # true
legend::Union{PlotLayoutLegend,Nothing} = nothing
annotations::Union{Vector{PlotAnnotation},Nothing} = nothing
geo::Union{PlotLayoutGeo,Nothing} = nothing
grid::Union{PlotLayoutGrid,Nothing} = nothing
mapbox::Union{PlotLayoutMapbox,Nothing} = nothing
margin_l::Union{Int,Nothing} = nothing # 80
margin_r::Union{Int,Nothing} = nothing # 80
margin_t::Union{Int,Nothing} = nothing # 100
margin_b::Union{Int,Nothing} = nothing # 80
margin_pad::Union{Int,Nothing} = nothing # 0
margin_autoexpand::Union{Bool,Nothing} = nothing # true
autosize::Union{Bool,Nothing} = nothing # true
width::Union{Int,String,Nothing} = nothing # 700
height::Union{Int,String,Nothing} = nothing # 450
font::Union{Font,Nothing} = nothing
uniformtext_mode::Union{String,Bool,Nothing} = nothing # false
uniformtext_minsize::Union{Int,Nothing} = nothing # 0
separators::Union{String,Nothing} = nothing # ".,"
paper_bgcolor::Union{String,Nothing} = nothing # "#fff"
plot_bgcolor::Union{String,Nothing} = nothing # "#fff"
# TODO: implement the following fields in function Stipple.render(pl::PlotLayout...
autotypenumbers::String = "convert types"
# TODO: colorscale settings
colorway::Vector{String} = ["#1f77b4", "#ff7f0e", "#2ca02c", "#d62728", "#9467bd",
"#8c564b", "#e377c2", "#7f7f7f", "#bcbd22", "#17becf"]
modebar_orientation::String = LAYOUT_ORIENTATION_HORIZONTAL
modebar_bgcolor::String = "transparent"
modebar_color::String = ""
modebar_activecolor::String = ""
# TODO: modebar_uirevision::String = ""
hovermode::Union{String,Bool} = "closest"
clickmode::String = "event"
dragmode::String = "zoom"
selectdirection::String = "any"
hoverdistance::Int = 20
spikedistance::Int = 20
hoverlabel_bgcolor::String = ""
hoverlabel_bordercolor::String = ""
hoverlabel_font::Font = Font()
hoverlabel_align::String = LAYOUT_AUTO
hoverlabel_namelength::Int = 15
transition_duration::Int = 500
transition_easing::String = "cubic-in-out"
transition_ordering::String = "layout first"
# TODO: datarevision
# TODO: editrevision
# TODO: selectionrevision
# TODO: template
# TODO: meta
# TODO: computed
calendar::String = "gregorian"
newshape_line_color::String = ""
newshape_line_width::Int = 4
newshape_line_dash::String = "solid"
newshape_fillcolor::String = "rgba(0,0,0,0)"
newshape_fillrule::String = "evenodd"
newshape_opacity::Float64 = 1.0
newshape_layer::String = LAYOUT_ABOVE
newshape_drawdirection::String = "diagonal"
activeshape_fillcolor::String = "rgb(255,0,255)"
activeshape_opacity::Float64 = 0.5
# TODO: hidesources
barmode::Union{String,Nothing} = nothing # LAYOUT_GROUP
barnorm::Union{String,Nothing} = nothing
bargap::Union{Float64,Nothing} = nothing # 0.5
bargroupgap::Union{Float64,Nothing} = nothing # 0
# TODO: hiddenlabels
# TODO: piecolorway
extendpiecolors::Bool = true
boxmode::String = LAYOUT_OVERLAY
boxgap::Float64 = 0.3
boxgroupgap::Float64 = 0.3
violinmode::String = LAYOUT_OVERLAY
violingap::Float64 = 0.3
violingroupgap::Float64 = 0.3
waterfallmode::String = LAYOUT_GROUP
waterfallgap::Float64 = 0.3
waterfallgroupgap::Float64 = 0.0
funnelmode::String = LAYOUT_STACK
funnelgap::Float64 = 0.0
funnelgroupgap::Float64 = 0.0
# TODO: funnelareacolorway
extendfunnelareacolors::Bool = true
# TODO: sunburstcolorway
extendsunburstcolors::Bool = true
# TODO: treemapcolorway
extendtreemapcolors::Bool = true
end
function Base.show(io::IO, l::PlotLayout)
default = PlotLayout()
output = "layout: \n"
for f in fieldnames(typeof(l))
prop = getproperty(l, f)
if prop != getproperty(default, f)
output *= "$f = $prop \n"
end
end
print(io, output)
end
function Base.Dict(pl::PlotLayout, fieldname::Union{Symbol,Nothing} = nothing)
layout = Dict{Symbol, Any}()
if pl.font !== nothing
layout[:font] = Dict{Symbol, Any}(
:family => pl.font.family,
:size => pl.font.size,
:color => pl.font.color
)
end
d1 = Dict{Symbol, Any}()
(pl.margin_l !== nothing) && (d1[:l] = pl.margin_l)
(pl.margin_r !== nothing) && (d1[:r] = pl.margin_r)
(pl.margin_t !== nothing) && (d1[:t] = pl.margin_t)
(pl.margin_b !== nothing) && (d1[:b] = pl.margin_b)
(pl.margin_pad !== nothing) && (d1[:pad] = pl.margin_pad)
(pl.margin_autoexpand !== nothing) && (d1[:autoexpand] = pl.margin_autoexpand)
(length(d1) > 0) && (layout[:margin] = d1)
d2 = Dict{Symbol, Any}()
(pl.uniformtext_mode !== nothing) && (d2[:mode] = pl.uniformtext_mode)
(pl.uniformtext_minsize !== nothing) && (d2[:minsize] = pl.uniformtext_minsize)
(length(d2) > 0) && (layout[:uniformtext] = d2)
(pl.title !== nothing) && (layout[:title] = Dict(pl.title))
(pl.legend !== nothing) && (layout[:legend] = Dict(pl.legend))
(pl.annotations !== nothing) && (layout[:annotations] = Dict.(pl.annotations))
(pl.grid !== nothing) && (layout[:grid] = Dict(pl.grid))
optionals!(layout, pl, [ :showlegend, :autosize, :separators, :paper_bgcolor, :plot_bgcolor,
:width, :height, :barmode, :barnorm, :bargap, :bargroupgap, :geo, :mapbox
])
if pl.xaxis !== nothing
for x in pl.xaxis
merge!(layout, Dict(x, "x"))
end
end
if pl.yaxis !== nothing
for y in pl.yaxis
merge!(layout, Dict(y, "y"))
end
end
if pl.axes !== nothing
for d in Dict.(pl.axes)
merge!(layout, d)
end
end
layout
end
function Stipple.render(pl::PlotLayout, fieldname::Union{Symbol,Nothing} = nothing)
Dict(pl)
end
function Stipple.render(pl::Vector{PlotLayout}, fieldname::Union{Symbol,Nothing} = nothing)
Dict.(pl)
end
end | StipplePlotly | https://github.com/GenieFramework/StipplePlotly.jl.git |
|
[
"MIT"
] | 0.14.3 | 9aee830051af43009b3c97651f124246fdabb86a | code | 2895 | module StipplePlotly
using Genie, Stipple, Stipple.Reexport, Stipple.ParsingTools
using Requires
import Genie: Assets.add_fileroute, Assets.asset_path
#===#
const assets_config = Genie.Assets.AssetsConfig(package = "StipplePlotly.jl")
_symbol_dict(x) = x
_symbol_dict(d::AbstractDict) =
Dict{Symbol,Any}([(Symbol(k), _symbol_dict(v)) for (k, v) in d])
#===#
function deps_routes() :: Nothing
Genie.Assets.external_assets(Stipple.assets_config) && return nothing
basedir = dirname(@__DIR__)
add_fileroute(assets_config, "plotly.min.js"; basedir, named = :get_plotlyjs)
add_fileroute(assets_config, "ResizeSensor.js"; basedir, named = :get_resizesensorjs)
add_fileroute(assets_config, "lodash.min.js"; basedir, named = :get_lodashjs)
add_fileroute(assets_config, "vueresize.min.js"; basedir, named = :get_vueresizejs)
add_fileroute(assets_config, "vueplotly.min.js"; basedir, named = :get_vueplotlyjs)
add_fileroute(assets_config, "sentinel.min.js"; basedir, named = :get_sentineljs)
add_fileroute(assets_config, "syncplot.js"; basedir, named = :get_syncplotjs)
nothing
end
function deps() :: Vector{String}
[
script(src = asset_path(assets_config, :js, file="plotly.min")),
script(src = asset_path(assets_config, :js, file="ResizeSensor")),
script(src = asset_path(assets_config, :js, file="lodash.min")),
script(src = asset_path(assets_config, :js, file="vueresize.min")),
script(src = asset_path(assets_config, :js, file="vueplotly.min")),
script(src = asset_path(assets_config, :js, file="sentinel.min")),
script(src = asset_path(assets_config, :js, file="syncplot"))
]
end
#===#
include("Charts.jl")
@reexport using .Charts
include("Layouts.jl")
@reexport using .Layouts
function __init__()
deps_routes()
Stipple.deps!(@__MODULE__, deps)
isdefined(Stipple, :register_global_components) && Stipple.register_global_components("plotly", legacy = true)
@require PlotlyBase = "a03496cd-edff-5a9b-9e67-9cda94a718b5" begin
@static if !isdefined(Base, :get_extension)
include("../ext/StipplePlotlyPlotlyBaseExt.jl")
end
export PBPlotWithEvents, PBPlotWithEventsReadOnly
Base.@kwdef struct PBPlotWithEvents
var""::R{PlotlyBase.Plot} = PlotlyBase.Plot()
_selected::R{Charts.PlotlyEvent} = Charts.PlotlyEvent()
_hover::R{Charts.PlotlyEvent} = Charts.PlotlyEvent()
_click::R{Charts.PlotlyEvent} = Charts.PlotlyEvent()
_relayout::R{Charts.PlotlyEvent} = Charts.PlotlyEvent()
end
Base.@kwdef struct PBPlotWithEventsReadOnly
var""::R{PlotlyBase.Plot} = PlotlyBase.Plot(), READONLY
_selected::R{Charts.PlotlyEvent} = Charts.PlotlyEvent()
_hover::R{Charts.PlotlyEvent} = Charts.PlotlyEvent()
_click::R{Charts.PlotlyEvent} = Charts.PlotlyEvent()
_relayout::R{Charts.PlotlyEvent} = Charts.PlotlyEvent()
end
end
end
end # module
| StipplePlotly | https://github.com/GenieFramework/StipplePlotly.jl.git |
|
[
"MIT"
] | 0.14.3 | 9aee830051af43009b3c97651f124246fdabb86a | code | 1415 | function create_example_dataframe()
xs = [1.0, 2.0, 3.0, 4.0]
ys = [10.0, 20.0, 30.0, 40.0]
groups = [1, 2, 1, 2]
labels = ["A", "C", "B", "D"]
return DataFrame(X = xs, Y = ys, Group = groups, Label = labels)
end
@testset "Scatter Plots" begin
@testset "Multiple Groups without Tooltips" begin
df = create_example_dataframe()
pd = plotdata(df, :X, :Y; groupfeature = :Group)
@test length(pd) == 2
@test length(pd[1].x) == length(pd[2].x)
@test length(pd[1].y) == length(pd[2].y)
@test isnothing(pd[1].text)
@test isnothing(pd[2].text)
end
@testset "Multiple Groups with Tooltips" begin
df = create_example_dataframe()
pd = plotdata(df, :X, :Y; groupfeature = :Group, text = df.Label)
@test length(pd) == 2
@test length(pd[1].x) == length(pd[2].x) == 2
@test length(pd[1].y) == length(pd[2].y) == 2
@test !isnothing(pd[1].text)
@test !isnothing(pd[2].text)
if !isnothing(pd[1].text) && !isnothing(pd[2].text)
@test length(pd[1].text) == length(pd[1].x) == length(pd[1].y) == 2
@test length(pd[2].text) == length(pd[2].x) == length(pd[2].x) == 2
@test pd[1].text[1] == "A"
@test pd[1].text[2] == "B"
@test pd[2].text[1] == "C"
@test pd[2].text[2] == "D"
end
end
end | StipplePlotly | https://github.com/GenieFramework/StipplePlotly.jl.git |
|
[
"MIT"
] | 0.14.3 | 9aee830051af43009b3c97651f124246fdabb86a | code | 2502 | @testset "PlotlyBase extension" begin
@testset "Stipple.JSONText" begin
@test ! @isdefined(PBPlotWithEvents) || @isdefined(PlotlyBase)
using PlotlyBase, PlotlyBase.JSON
@test @isdefined PBPlotWithEvents
sc = scatter(x = StipplePlotly.JSONText("jsontext"), more_of_this = "a")
pl = Plot(sc)
@test JSON.json(sc) == "{\"type\":\"scatter\",\"more\":{\"of\":{\"this\":\"a\"}},\"x\":jsontext}"
@test contains(JSON.json(pl), "{\"type\":\"scatter\",\"more\":{\"of\":{\"this\":\"a\"}},\"x\":jsontext}")
@test Stipple.json(sc) == "{\"type\":\"scatter\",\"more\":{\"of\":{\"this\":\"a\"}},\"x\":jsontext}"
@test contains(Stipple.json(pl), "{\"type\":\"scatter\",\"more\":{\"of\":{\"this\":\"a\"}},\"x\":jsontext}")
end
@testset "Parsing" begin
using Stipple
import Stipple.stipple_parse
@testset "Layout" begin
pl = PlotlyBase.Layout(xaxis_range = [1, 2])
pl_d = JSON3.read(Stipple.json(render(pl)), Dict)
pl_in = stipple_parse(PlotlyBase.Layout, pl_d)
@test pl_in[:xaxis_range] == [1, 2]
pl_in = stipple_parse(PlotlyBase.Layout{Dict{Symbol, Any}}, pl_d)
pl_in[:xaxis_range] == [1, 2]
@static if VersionNumber(Genie.Assets.package_version(Stipple)) >= v"0.30.6"
pl_in = stipple_parse(PlotlyBase.Layout{OrderedDict{Symbol, Any}}, pl_d)
@test pl_in[:xaxis_range] == [1, 2]
end
end
@testset "GenericTrace" begin
tr = scatter(x = [1, 2, 3], y = [3, 4, 5])
tr_d = JSON3.read(Stipple.json(render(tr)), Dict)
tr_in = stipple_parse(GenericTrace, tr_d)
@test tr_in.x == [1, 2, 3]
@test tr_in.y == [3, 4, 5]
end
@testset "Plot" begin
pl = PlotlyBase.Plot([scatter(x = [1, 2, 3], y = [3, 4, 5])], PlotlyBase.Layout(xaxis_range = [1, 2]))
pl_d = JSON3.read(Stipple.json(render(pl)), Dict)
pl_in = stipple_parse(PlotlyBase.Plot, pl_d)
@test length(pl_in.data) == 1
@test pl_in.layout[:xaxis_range] == [1, 2]
PlotType = typeof(Plot())
pl_in = stipple_parse(PlotType, pl_d)
@test length(pl_in.data) == 1
@test pl_in.data[1][:x] == [1, 2, 3]
@test pl_in.layout[:xaxis_range] == [1, 2]
end
end
end
pl = PlotlyBase.Layout(xaxis_range = [1, 2]) | StipplePlotly | https://github.com/GenieFramework/StipplePlotly.jl.git |
|
[
"MIT"
] | 0.14.3 | 9aee830051af43009b3c97651f124246fdabb86a | code | 275 | using StipplePlotly
using Stipple
using Test
using DataFrames
files = filter(endswith(".jl"), readdir(@__DIR__))
for file in files
file == "runtests.jl" && continue
title = file[1:end-3]
@testset verbose = true "$title" begin
include(file)
end
end
| StipplePlotly | https://github.com/GenieFramework/StipplePlotly.jl.git |
|
[
"MIT"
] | 0.14.3 | 9aee830051af43009b3c97651f124246fdabb86a | docs | 2349 | # StipplePlotly
Embedding Plotly Charts in Stipple.
### News: The standard API is now PlotlyBase, the StipplePlotly API is considered legacy.
### Example with forwarding of plotly events
See the docstrings of `watchplots()` and `watchplot()` for more details!
```julia
using Stipple, Stipple.ReactiveTools
using StipplePlotly
using PlotlyBase
@app Example begin
@mixin plot::PBPlotWithEvents
@in plot_cursor = Dict{String, Any}()
@onchange isready begin
isready || return
p = Plot(scatter(y=1:10))
plot.layout = p.layout
plot.data = p.data
end
@onchange plot_selected begin
haskey(plot_selected, "points") && @info "Selection: $(getindex.(plot_selected["points"], "pointIndex"))"
end
@onchange plot_click begin
@info "$plot_click"
end
@onchange plot_hover begin
@info "hovered over $(plot_hover["points"][1]["x"]):$(plot_hover["points"][1]["y"])"
# @info "$plot_hover"
end
@onchange plot_cursor begin
@info "cursor moved to $(plot_cursor["cursor"]["x"]):$(plot_cursor["cursor"]["y"])"
# @info "$plot_cursor"
end
end
# commented lines below: manual definition of plot_events
# @app Example begin
# @in plot = Plot()
# @in plot_selected = Dict{String, Any}()
# @in plot_click = Dict{String, Any}()
# @in plot_hover = Dict{String, Any}()
# @in plot_cursor = Dict{String, Any}()
# end
Stipple.js_mounted(::Example) = watchplots()
# the keyword argument 'keepselection' (default = false) controls whether the selection outline shall be removed after selection
function ui()
cell(class = "st-module", [
plotly(:plot, syncevents = true, keepselection = false),
])
end
@page("/", ui, model = Example)
```
Possible forwarded events are
- '_selected' (Selection changed)
- '_hover' (hovered over data point)
- '_click' (click event on plot area)
- '_relayout' (plot layout changed)
- '_cursor' (current mouse position, not covered in PBPlotWithEvents in order to reduce data traffic)
For more Stipple Plotly Demos please check: [Stipple Demos Repo](https://github.com/GenieFramework/StippleDemos)
## Acknowledgement
Handling of Plotly Events was highly inspired by the [PlotlyJS](https://github.com/JuliaPlots/PlotlyJS.jl) package by [Spencer Lyon](https://github.com/sglyon)
| StipplePlotly | https://github.com/GenieFramework/StipplePlotly.jl.git |
|
[
"MIT"
] | 0.14.3 | 9aee830051af43009b3c97651f124246fdabb86a | docs | 48 | # StipplePlotly
Plotting library for Stipple.jl | StipplePlotly | https://github.com/GenieFramework/StipplePlotly.jl.git |
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